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@article{DBLP:journals/biodatamining/SrithanyaratTSRLL24,
author = {Thanyawee Srithanyarat and
Kittisak Taoma and
Thana Sutthibutpong and
Marasri Ruengjitchatchawalya and
Monrudee Liangruksa and
Teeraphan Laomettachit},
title = {Interpreting drug synergy in breast cancer with deep learning using
target-protein inhibition profiles},
journal = {BioData Min.},
volume = {17},
number = {1},
year = {2024},
url = {https://doi.org/10.1186/s13040-024-00359-z},
doi = {10.1186/S13040-024-00359-Z},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodatamining/SrithanyaratTSRLL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/OdunitanSAOBAAOMAAA24,
author = {Tope T. Odunitan and
Oluwatosin A. Saibu and
Boluwatife T. Apanisile and
Damilola A. Omoboyowa and
Toheeb A. Balogun and
Adeyoola V. Awe and
Temitope M. Ajayi and
Grace V. Olagunju and
Fatimah M. Mahmoud and
Modinat Akinboade and
Catherine B. Adeniji and
Waliu O. Abdulazeez},
title = {Integrating biocomputational techniques for Breast cancer drug discovery
via the HER-2, BCRA, {VEGF} and {ER} protein targets},
journal = {Comput. Biol. Medicine},
volume = {168},
pages = {107737},
year = {2024},
url = {https://doi.org/10.1016/j.compbiomed.2023.107737},
doi = {10.1016/J.COMPBIOMED.2023.107737},
timestamp = {Sat, 10 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cbm/OdunitanSAOBAAOMAAA24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/ChauhanGSP24a,
author = {Shweta Singh Chauhan and
Anshika Gupta and
Aashna Srivastava and
Ramakrishnan Parthasarathi},
title = {Discovering targeted inhibitors for \emph{Escherichia coli} efflux
pump fusion proteins using computational and structure-guided approaches},
journal = {J. Comput. Chem.},
volume = {45},
number = {1},
pages = {13--24},
year = {2024},
url = {https://doi.org/10.1002/jcc.27215},
doi = {10.1002/JCC.27215},
timestamp = {Sun, 10 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcc/ChauhanGSP24a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/GartanKMVCHBBR24,
author = {Parveen Gartan and
Fahimeh Khorsand and
Pushpak Mizar and
Juha Ilmari Vahokovski and
Luis F. Cervantes and
Bengt Erik Haug and
Ruth Brenk and
Charles L. Brooks III and
Nathalie Reuter},
title = {Investigating Polypharmacology through Targeting Known Human Neutrophil
Elastase Inhibitors to Proteinase 3},
journal = {J. Chem. Inf. Model.},
volume = {64},
number = {3},
pages = {621--626},
year = {2024},
url = {https://doi.org/10.1021/acs.jcim.3c01949},
doi = {10.1021/ACS.JCIM.3C01949},
timestamp = {Fri, 08 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/GartanKMVCHBBR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/MatsukiyoYY24,
author = {Yuki Matsukiyo and
Chikashige Yamanaka and
Yoshihiro Yamanishi},
title = {\emph{De Novo} Generation of Chemical Structures of Inhibitor and
Activator Candidates for Therapeutic Target Proteins by a Transformer-Based
Variational Autoencoder and Bayesian Optimization},
journal = {J. Chem. Inf. Model.},
volume = {64},
number = {7},
pages = {2345--2355},
year = {2024},
url = {https://doi.org/10.1021/acs.jcim.3c00824},
doi = {10.1021/ACS.JCIM.3C00824},
timestamp = {Fri, 17 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/MatsukiyoYY24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mlst/NgoH24,
author = {Nhat Khang Ngo and
Truong Son Hy},
title = {Multimodal protein representation learning and target-aware variational
auto-encoders for protein-binding ligand generation},
journal = {Mach. Learn. Sci. Technol.},
volume = {5},
number = {2},
pages = {25021},
year = {2024},
url = {https://doi.org/10.1088/2632-2153/ad3ee4},
doi = {10.1088/2632-2153/AD3EE4},
timestamp = {Fri, 17 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mlst/NgoH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tetc/BacciuEGMPS24,
author = {Davide Bacciu and
Federico Errica and
Alessio Gravina and
Lorenzo Madeddu and
Marco Podda and
Giovanni Stilo},
title = {Deep Graph Networks for Drug Repurposing With Multi-Protein Targets},
journal = {{IEEE} Trans. Emerg. Top. Comput.},
volume = {12},
number = {1},
pages = {177--189},
year = {2024},
url = {https://doi.org/10.1109/TETC.2023.3238963},
doi = {10.1109/TETC.2023.3238963},
timestamp = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tetc/BacciuEGMPS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/comsnets/SimonB24,
author = {Essmily Simon and
Sanjay S. Bankapur},
title = {Prediction of Drug-Target Interactions Using {BERT} for Protein Sequences
and Drug Compound},
booktitle = {16th International Conference on COMmunication Systems {\&} NETworkS,
{COMSNETS} 2024, Bengaluru, India, January 3-7, 2024},
pages = {436--438},
publisher = {{IEEE}},
year = {2024},
url = {https://doi.org/10.1109/COMSNETS59351.2024.10427536},
doi = {10.1109/COMSNETS59351.2024.10427536},
timestamp = {Fri, 01 Mar 2024 14:04:41 +0100},
biburl = {https://dblp.org/rec/conf/comsnets/SimonB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/MijitWLXCX23,
author = {Arzu Mijit and
Xiaona Wang and
Yanlin Li and
Hangwei Xu and
Yingjun Chen and
Weiwei Xue},
title = {Mapping synthetic binding proteins epitopes on diverse protein targets
by protein structure prediction and protein-protein docking},
journal = {Comput. Biol. Medicine},
volume = {163},
pages = {107183},
year = {2023},
url = {https://doi.org/10.1016/j.compbiomed.2023.107183},
doi = {10.1016/J.COMPBIOMED.2023.107183},
timestamp = {Sun, 24 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/MijitWLXCX23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/WuWZMSLYZYWXZ23,
author = {Leyun Wu and
Guangpu Wang and
Liping Zhou and
Mengxia Mo and
Yulong Shi and
Bo Li and
Leimiao Yin and
Qiang Zhao and
Yongqing Yang and
Chengkun Wu and
Zhijian Xu and
Weiliang Zhu},
title = {Molecular dynamics study on the behavior and binding mechanism of
target protein Transgelin-2 with its agonist {TSG12} for anti-asthma
drug discovery},
journal = {Comput. Biol. Medicine},
volume = {153},
pages = {106515},
year = {2023},
url = {https://doi.org/10.1016/j.compbiomed.2022.106515},
doi = {10.1016/J.COMPBIOMED.2022.106515},
timestamp = {Tue, 28 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/WuWZMSLYZYWXZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cmpb/SinghP23,
author = {Rahul Singh and
Rituraj Purohit},
title = {Computational analysis of protein-ligand interaction by targeting
a cell cycle restrainer},
journal = {Comput. Methods Programs Biomed.},
volume = {231},
pages = {107367},
year = {2023},
url = {https://doi.org/10.1016/j.cmpb.2023.107367},
doi = {10.1016/J.CMPB.2023.107367},
timestamp = {Tue, 28 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cmpb/SinghP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/KalathingalR23,
author = {Mahroof Kalathingal and
Young Min Rhee},
title = {Molecular mechanism of binding between a therapeutic {RNA} aptamer
and its protein target {VEGF:} {A} molecular dynamics study},
journal = {J. Comput. Chem.},
volume = {44},
number = {11},
pages = {1129--1137},
year = {2023},
url = {https://doi.org/10.1002/jcc.27070},
doi = {10.1002/JCC.27070},
timestamp = {Sun, 16 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/KalathingalR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/ChenWWWLCZYS23,
author = {Yangyang Chen and
Zixu Wang and
Lei Wang and
Jianmin Wang and
Pengyong Li and
Dongsheng Cao and
Xiangxiang Zeng and
Xiucai Ye and
Tetsuya Sakurai},
title = {Deep generative model for drug design from protein target sequence},
journal = {J. Cheminformatics},
volume = {15},
number = {1},
pages = {38},
year = {2023},
url = {https://doi.org/10.1186/s13321-023-00702-2},
doi = {10.1186/S13321-023-00702-2},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/ChenWWWLCZYS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/YangZGZHSLHC23,
author = {Su{-}Qing Yang and
Liu{-}Xia Zhang and
You{-}Jin Ge and
Jin{-}Wei Zhang and
Jian{-}Xin Hu and
Cheng{-}Ying Shen and
Ai{-}Ping Lu and
Tingjun Hou and
Dong{-}Sheng Cao},
title = {In-silico target prediction by ensemble chemogenomic model based on
multi-scale information of chemical structures and protein sequences},
journal = {J. Cheminformatics},
volume = {15},
number = {1},
pages = {48},
year = {2023},
url = {https://doi.org/10.1186/s13321-023-00720-0},
doi = {10.1186/S13321-023-00720-0},
timestamp = {Thu, 08 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/YangZGZHSLHC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/AlhamwiAS23,
author = {Almotasem Belah Alhamwi and
Canan Atilgan and
{\"{O}}zge Sensoy},
title = {Nonlocal Effects of Antibiotic-Resistance-Causing Mutations Reveal
an Alternative Region for Targeting on FtsW-Penicillin-Binding Protein
3 Complex of \emph{Haemophilus influenzae}},
journal = {J. Chem. Inf. Model.},
volume = {63},
number = {10},
pages = {3094--3104},
year = {2023},
url = {https://doi.org/10.1021/acs.jcim.3c00127},
doi = {10.1021/ACS.JCIM.3C00127},
timestamp = {Fri, 02 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/AlhamwiAS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/KurniawanI23,
author = {Jason Kurniawan and
Takashi Ishida},
title = {Comparing Supervised Learning and Rigorous Approach for Predicting
Protein Stability upon Point Mutations in Difficult Targets},
journal = {J. Chem. Inf. Model.},
volume = {63},
number = {21},
pages = {6778--6788},
year = {2023},
url = {https://doi.org/10.1021/acs.jcim.3c00750},
doi = {10.1021/ACS.JCIM.3C00750},
timestamp = {Sun, 17 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/KurniawanI23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/MostofianMRPASI23,
author = {Barmak Mostofian and
Holli{-}Joi Martin and
Asghar Razavi and
Shivam Patel and
Bryce K. Allen and
Woody Sherman and
Jesus A. Izaguirre},
title = {Targeted Protein Degradation: Advances, Challenges, and Prospects
for Computational Methods},
journal = {J. Chem. Inf. Model.},
volume = {63},
number = {17},
pages = {5408--5432},
year = {2023},
url = {https://doi.org/10.1021/acs.jcim.3c00603},
doi = {10.1021/ACS.JCIM.3C00603},
timestamp = {Sat, 14 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/MostofianMRPASI23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/DuartePereiraMOS23,
author = {Sara Duarte{-}Pereira and
S{\'{e}}rgio Matos and
Jos{\'{e}} Lu{\'{\i}}s Oliveira and
Raquel M. Silva},
title = {Study of NAD-interacting proteins highlights the extent of {NAD} regulatory
roles in the cell and its potential as a therapeutic target},
journal = {J. Integr. Bioinform.},
volume = {20},
number = {2},
year = {2023},
url = {https://doi.org/10.1515/jib-2022-0049},
doi = {10.1515/JIB-2022-0049},
timestamp = {Sat, 02 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/DuartePereiraMOS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mbec/ChattopadhyayDFC23,
author = {Subhagata Chattopadhyay and
Nhat Phuong Do and
Darren R. Flower and
Amit K. Chattopadhyay},
title = {Extracting prime protein targets as possible drug candidates: machine
learning evaluation},
journal = {Medical Biol. Eng. Comput.},
volume = {61},
number = {11},
pages = {3035--3048},
year = {2023},
url = {https://doi.org/10.1007/s11517-023-02893-0},
doi = {10.1007/S11517-023-02893-0},
timestamp = {Wed, 01 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/mbec/ChattopadhyayDFC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/MarinoNCFDXAM23,
author = {Giacomo B. Marino and
Michael Ngai and
Daniel J. B. Clarke and
Reid H. Fleishman and
Eden Z. Deng and
Zhuorui Xie and
Nasheath Ahmed and
Avi Ma'ayan},
title = {GeneRanger and TargetRanger: processed gene and protein expression
levels across cells and tissues for target discovery},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{W1}},
pages = {213--224},
year = {2023},
url = {https://doi.org/10.1093/nar/gkad399},
doi = {10.1093/NAR/GKAD399},
timestamp = {Sat, 19 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/MarinoNCFDXAM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/netmahib/RanjanKKAM23,
author = {Amit Ranjan and
Hritik Kumar and
Deepshikha Kumari and
Archit Anand and
Rajiv Misra},
title = {Molecule generation toward target protein (SARS-CoV-2) using reinforcement
learning-based graph neural network via knowledge graph},
journal = {Netw. Model. Anal. Health Informatics Bioinform.},
volume = {12},
number = {1},
pages = {13},
year = {2023},
url = {https://doi.org/10.1007/s13721-023-00409-2},
doi = {10.1007/S13721-023-00409-2},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/netmahib/RanjanKKAM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/0002023,
author = {Li Xie and
Lei Xie},
title = {Elucidation of genome-wide understudied proteins targeted by PROTAC-induced
degradation using interpretable machine learning},
journal = {PLoS Comput. Biol.},
volume = {19},
number = {8},
year = {2023},
url = {https://doi.org/10.1371/journal.pcbi.1010974},
doi = {10.1371/JOURNAL.PCBI.1010974},
timestamp = {Sat, 14 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/0002023.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/titb/MaZLJWGLBJW23,
author = {Wenjian Ma and
Shugang Zhang and
Zhen Li and
Mingjian Jiang and
Shuang Wang and
Nianfan Guo and
Yuanfei Li and
Xiangpeng Bi and
Huasen Jiang and
Zhiqiang Wei},
title = {Predicting Drug-Target Affinity by Learning Protein Knowledge From
Biological Networks},
journal = {{IEEE} J. Biomed. Health Informatics},
volume = {27},
number = {4},
pages = {2128--2137},
year = {2023},
url = {https://doi.org/10.1109/JBHI.2023.3240305},
doi = {10.1109/JBHI.2023.3240305},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/titb/MaZLJWGLBJW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/ShiMGXCW23,
author = {Wenqi Shi and
Mio Murakoso and
Xiaoyan Guo and
Linxi Xiong and
Matthew Chen and
May D. Wang},
editor = {Xingpeng Jiang and
Haiying Wang and
Reda Alhajj and
Xiaohua Hu and
Felix Engel and
Mufti Mahmud and
Nadia Pisanti and
Xuefeng Cui and
Hong Song},
title = {Effective Surrogate Models for Docking Scores Prediction of Candidate
Drug Molecules on SARS-CoV-2 Protein Targets},
booktitle = {{IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2023, Istanbul, Turkiye, December 5-8, 2023},
pages = {4235--4242},
publisher = {{IEEE}},
year = {2023},
url = {https://doi.org/10.1109/BIBM58861.2023.10385643},
doi = {10.1109/BIBM58861.2023.10385643},
timestamp = {Thu, 14 Mar 2024 16:59:09 +0100},
biburl = {https://dblp.org/rec/conf/bibm/ShiMGXCW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fpl/ChenZYW23,
author = {Ruiqi Chen and
Haoyang Zhang and
Jun Yu and
Kun Wang},
editor = {Nele Mentens and
Leonel Sousa and
Pedro Trancoso and
Nikela Papadopoulou and
Ioannis Sourdis},
title = {{FPGA} Accelerating Multi-Source Transfer Learning with {GAT} for
Bioactivities of Ligands Targeting Orphan {G} Protein-Coupled Receptors},
booktitle = {33rd International Conference on Field-Programmable Logic and Applications,
{FPL} 2023, Gothenburg, Sweden, September 4-8, 2023},
pages = {317--321},
publisher = {{IEEE}},
year = {2023},
url = {https://doi.org/10.1109/FPL60245.2023.00054},
doi = {10.1109/FPL60245.2023.00054},
timestamp = {Mon, 13 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fpl/ChenZYW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icai4/WuLPZC23,
author = {Yijia Wu and
Yanmei Lin and
Yuzhong Peng and
Ru Zhang and
Li Cai},
editor = {De{-}Shuang Huang and
Prashan Premaratne and
Changan Yuan},
title = {T-GraphDTA: {A} Drug-Target Binding Affinity Prediction Framework
Based on Protein Pre-training Model and Hybrid Graph Neural Network},
booktitle = {Applied Intelligence - First International Conference, {ICAI} 2023,
Nanning, China, December 8-12, 2023, Proceedings, Part {I}},
series = {Communications in Computer and Information Science},
volume = {2014},
pages = {113--123},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-981-97-0903-8\_12},
doi = {10.1007/978-981-97-0903-8\_12},
timestamp = {Wed, 15 May 2024 16:44:20 +0200},
biburl = {https://dblp.org/rec/conf/icai4/WuLPZC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icic/ZhangZJCW23,
author = {Runhua Zhang and
Baozhong Zhu and
Tengsheng Jiang and
Zhiming Cui and
Hongjie Wu},
editor = {De{-}Shuang Huang and
Prashan Premaratne and
Baohua Jin and
Boyang Qu and
Kang{-}Hyun Jo and
Abir Hussain},
title = {Deep Learning-Based Prediction of Drug-Target Binding Affinities by
Incorporating Local Structure of Protein},
booktitle = {Advanced Intelligent Computing Technology and Applications - 19th
International Conference, {ICIC} 2023, Zhengzhou, China, August 10-13,
2023, Proceedings, Part {III}},
series = {Lecture Notes in Computer Science},
volume = {14088},
pages = {666--675},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-981-99-4749-2\_57},
doi = {10.1007/978-981-99-4749-2\_57},
timestamp = {Tue, 08 Aug 2023 13:15:20 +0200},
biburl = {https://dblp.org/rec/conf/icic/ZhangZJCW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icit/HuLLZZZ23,
author = {Xiuyuan Hu and
Yanghepu Li and
Guoqing Liu and
Yang Zhao and
Hao Zhang and
Liang Zhao},
title = {De novo Drug Design against SARS-CoV-2 Protein Targets using SMILES-based
Deep Reinforcement Learning},
booktitle = {Proceedings of the 2023 11th International Conference on Information
Technology: IoT and Smart City, {ICIT} 2023, Kyoto, Japan, December
14-17, 2023},
pages = {161--166},
publisher = {{ACM}},
year = {2023},
url = {https://doi.org/10.1145/3638985.3639012},
doi = {10.1145/3638985.3639012},
timestamp = {Thu, 25 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icit/HuLLZZZ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iclr/ZhangMZ023,
author = {Zaixi Zhang and
Yaosen Min and
Shuxin Zheng and
Qi Liu},
title = {Molecule Generation For Target Protein Binding with Structural Motifs},
booktitle = {The Eleventh International Conference on Learning Representations,
{ICLR} 2023, Kigali, Rwanda, May 1-5, 2023},
publisher = {OpenReview.net},
year = {2023},
url = {https://openreview.net/pdf?id=Rq13idF0F73},
timestamp = {Fri, 30 Jun 2023 14:38:38 +0200},
biburl = {https://dblp.org/rec/conf/iclr/ZhangMZ023.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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author = {Jiahui Wen and
Haitao Gan and
Zhi Yang and
Ming Shi and
Ji Wang},
editor = {Biao Luo and
Long Cheng and
Zheng{-}Guang Wu and
Hongyi Li and
Chaojie Li},
title = {MView-DTI: {A} Multi-view Feature Fusion-Based Approach for Drug-Target
Protein Interaction Prediction},
booktitle = {Neural Information Processing - 30th International Conference, {ICONIP}
2023, Changsha, China, November 20-23, 2023, Proceedings, Part {X}},
series = {Communications in Computer and Information Science},
volume = {1964},
pages = {400--411},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-981-99-8141-0\_30},
doi = {10.1007/978-981-99-8141-0\_30},
timestamp = {Mon, 27 Nov 2023 17:35:45 +0100},
biburl = {https://dblp.org/rec/conf/iconip/WenG0SW23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@inproceedings{DBLP:conf/ijcnn/ChhariaSN23,
author = {Aviral Chharia and
Runjhun Saran and
Apurva Narayan},
title = {cAPTured: Neural Reflex Arc-Inspired Fuzzy Continual Learning for
Capturing in Silico Aptamer-Target Protein Interactions},
booktitle = {International Joint Conference on Neural Networks, {IJCNN} 2023, Gold
Coast, Australia, June 18-23, 2023},
pages = {1--9},
publisher = {{IEEE}},
year = {2023},
url = {https://doi.org/10.1109/IJCNN54540.2023.10191809},
doi = {10.1109/IJCNN54540.2023.10191809},
timestamp = {Wed, 09 Aug 2023 16:25:09 +0200},
biburl = {https://dblp.org/rec/conf/ijcnn/ChhariaSN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@article{DBLP:journals/corr/abs-2306-13957,
author = {Lei Huang and
Zheng Yuan and
Huihui Yan and
Rong Sheng and
Linjing Liu and
Fuzhou Wang and
Weidun Xie and
Nanjun Chen and
Fei Huang and
Songfang Huang and
Ka{-}Chun Wong and
Yaoyun Zhang},
title = {DiffDTM: {A} conditional structure-free framework for bioactive molecules
generation targeted for dual proteins},
journal = {CoRR},
volume = {abs/2306.13957},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2306.13957},
doi = {10.48550/ARXIV.2306.13957},
eprinttype = {arXiv},
eprint = {2306.13957},
timestamp = {Tue, 27 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2306-13957.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2309-16685,
author = {Nhat Khang Ngo and
Truong Son Hy},
title = {Target-aware Variational Auto-encoders for Ligand Generation with
Multimodal Protein Representation Learning},
journal = {CoRR},
volume = {abs/2309.16685},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2309.16685},
doi = {10.48550/ARXIV.2309.16685},
eprinttype = {arXiv},
eprint = {2309.16685},
timestamp = {Tue, 17 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2309-16685.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2310-04017,
author = {Rakesh Bal and
Yijia Xiao and
Wei Wang},
title = {PGraphDTA: Improving Drug Target Interaction Prediction using Protein
Language Models and Contact Maps},
journal = {CoRR},
volume = {abs/2310.04017},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2310.04017},
doi = {10.48550/ARXIV.2310.04017},
eprinttype = {arXiv},
eprint = {2310.04017},
timestamp = {Fri, 20 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2310-04017.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChaiGYLLCSYWXY22,
author = {Mengya Chai and
Yajuan Guo and
Liu Yang and
Jianhui Li and
Shuo Liu and
Lei Chen and
Yuelei Shen and
Yi Yang and
Youchun Wang and
Lida Xu and
Changyuan Yu},
title = {A high-throughput single cell-based antibody discovery approach against
the full-length SARS-CoV-2 spike protein suggests a lack of neutralizing
antibodies targeting the highly conserved {S2} domain},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac070},
doi = {10.1093/BIB/BBAC070},
timestamp = {Thu, 02 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChaiGYLLCSYWXY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/YinHYJHW22,
author = {Yueming Yin and
Haifeng Hu and
Zhen Yang and
Feihu Jiang and
Yihe Huang and
Jiansheng Wu},
title = {{AFSE:} towards improving model generalization of deep graph learning
of ligand bioactivities targeting {GPCR} proteins},
journal = {Briefings Bioinform.},
volume = {23},
number = {3},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac077},
doi = {10.1093/BIB/BBAC077},
timestamp = {Tue, 31 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/YinHYJHW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChatzigoulasC22,
author = {Alexios Chatzigoulas and
Zoe Cournia},
title = {{DREAMM:} a web-based server for drugging protein-membrane interfaces
as a novel workflow for targeted drug design},
journal = {Bioinform.},
volume = {38},
number = {24},
pages = {5449--5451},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac680},
doi = {10.1093/BIOINFORMATICS/BTAC680},
timestamp = {Sat, 13 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChatzigoulasC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WangLW22,
author = {Shiming Wang and
Jie Li and
Yadong Wang},
title = {{M2PP:} a novel computational model for predicting drug-targeted pathogenic
proteins},
journal = {{BMC} Bioinform.},
volume = {23},
number = {1},
pages = {7},
year = {2022},
url = {https://doi.org/10.1186/s12859-021-04522-9},
doi = {10.1186/S12859-021-04522-9},
timestamp = {Thu, 07 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WangLW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/XiaXXWWHSG22,
author = {Shengrong Xia and
Yingchun Xia and
Chulei Xiang and
Hui Wang and
Chao Wang and
Jin He and
Guolong Shi and
Lichuan Gu},
title = {A virus-target host proteins recognition method based on integrated
complexes data and seed extension},
journal = {{BMC} Bioinform.},
volume = {23},
number = {1},
pages = {256},
year = {2022},
url = {https://doi.org/10.1186/s12859-022-04792-x},
doi = {10.1186/S12859-022-04792-X},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/XiaXXWWHSG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/KarasevSLFP22,
author = {Dmitry A. Karasev and
Boris Sobolev and
Alexey Lagunin and
Dmitry Filimonov and
Vladimir Poroikov},
title = {The method predicting interaction between protein targets and small-molecular
ligands with the wide applicability domain},
journal = {Comput. Biol. Chem.},
volume = {98},
pages = {107674},
year = {2022},
url = {https://doi.org/10.1016/j.compbiolchem.2022.107674},
doi = {10.1016/J.COMPBIOLCHEM.2022.107674},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/KarasevSLFP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/AliKPKBD22,
author = {Farman Ali and
Harish Kumar and
Shruti Patil and
Ketan Kotecha and
Ameen Banjar and
Ali Daud},
title = {Target-DBPPred: An intelligent model for prediction of DNA-binding
proteins using discrete wavelet transform based compression and light
eXtreme gradient boosting},
journal = {Comput. Biol. Medicine},
volume = {145},
pages = {105533},
year = {2022},
url = {https://doi.org/10.1016/j.compbiomed.2022.105533},
doi = {10.1016/J.COMPBIOMED.2022.105533},
timestamp = {Sun, 30 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/AliKPKBD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/DwivediMYD22,
author = {Manish Dwivedi and
Sutanu Mukhopadhyay and
Shalini Yadav and
Kshatresh Dutta Dubey},
title = {A multidrug efflux protein in \emph{Mycobacterium tuberculosis}; tap
as a potential drug target for drug repurposing},
journal = {Comput. Biol. Medicine},
volume = {146},
pages = {105607},
year = {2022},
url = {https://doi.org/10.1016/j.compbiomed.2022.105607},
doi = {10.1016/J.COMPBIOMED.2022.105607},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/DwivediMYD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/EskandarzadeGSD22,
author = {Neda Eskandarzade and
Abozar Ghorbani and
Samira Samarfard and
Jose Diaz and
Pietro H. Guzzi and
Niloofar Fariborzi and
Ahmad Tahmasebi and
Keramatollah Izadpanah},
title = {Network for network concept offers new insights into host- SARS-CoV-2
protein interactions and potential novel targets for developing antiviral
drugs},
journal = {Comput. Biol. Medicine},
volume = {146},
pages = {105575},
year = {2022},
url = {https://doi.org/10.1016/j.compbiomed.2022.105575},
doi = {10.1016/J.COMPBIOMED.2022.105575},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/EskandarzadeGSD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/MaYWZSHXZ22,
author = {Minfei Ma and
Yanqing Yang and
Leyun Wu and
Liping Zhou and
Yulong Shi and
Jiaxin Han and
Zhijian Xu and
Weiliang Zhu},
title = {Conserved protein targets for developing pan-coronavirus drugs based
on sequence and 3D structure similarity analyses},
journal = {Comput. Biol. Medicine},
volume = {145},
pages = {105455},
year = {2022},
url = {https://doi.org/10.1016/j.compbiomed.2022.105455},
doi = {10.1016/J.COMPBIOMED.2022.105455},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/MaYWZSHXZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/YuQLHYZWYWXZWZZ22,
author = {Jianhai Yu and
Zhiran Qin and
Xuling Liu and
Xiaoen He and
Jinxiu Yao and
Xuan Zhou and
Kun Wen and
Nan Yu and
Qinghua Wu and
Weiwei Xiao and
Li Zhu and
Chengsong Wan and
Bao Zhang and
Wei Zhao},
title = {High-specificity targets in SARS-CoV-2 {N} protein for serological
detection and distinction from SARS-CoV},
journal = {Comput. Biol. Medicine},
volume = {143},
pages = {105272},
year = {2022},
url = {https://doi.org/10.1016/j.compbiomed.2022.105272},
doi = {10.1016/J.COMPBIOMED.2022.105272},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/YuQLHYZWYWXZWZZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fbinf/GallettiAOF22,
author = {Cristiano Galletti and
Joaquim Aguirre{-}Plans and
Baldo Oliva and
Narcis Fernandez{-}Fuentes},
title = {Prediction of Adverse Drug Reaction Linked to Protein Targets Using
Network-Based Information and Machine Learning},
journal = {Frontiers Bioinform.},
volume = {2},
year = {2022},
url = {https://doi.org/10.3389/fbinf.2022.906644},
doi = {10.3389/FBINF.2022.906644},
timestamp = {Fri, 28 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fbinf/GallettiAOF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/gpb/LiuLJLGHLQYHL22,
author = {Zhongyang Liu and
Honglei Li and
Zhaoyu Jin and
Yang Li and
Feifei Guo and
Yangzhige He and
Xinyue Liu and
Yaning Qi and
Liying Yuan and
Fuchu He and
Dong Li},
title = {Exploration of Target Spaces in the Human Genome for Protein and Peptide
Drugs},
journal = {Genom. Proteom. Bioinform.},
volume = {20},
number = {4},
pages = {780--794},
year = {2022},
url = {https://doi.org/10.1016/j.gpb.2021.10.007},
doi = {10.1016/J.GPB.2021.10.007},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/gpb/LiuLJLGHLQYHL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/gpb/ZhangBCDCSZZGZLFTL22,
author = {Wubing Zhang and
Shourya S. Roy Burman and
Jiaye Chen and
Katherine A. Donovan and
Yang Cao and
Chelsea Shu and
Boning Zhang and
Zexian Zeng and
Shengqing Gu and
Yi Zhang and
Dian Li and
Eric S. Fischer and
Collin Tokheim and
X. Shirley Liu},
title = {Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability
of Targeted Protein Degradation},
journal = {Genom. Proteom. Bioinform.},
volume = {20},
number = {5},
pages = {882--898},
year = {2022},
url = {https://doi.org/10.1016/j.gpb.2022.11.008},
doi = {10.1016/J.GPB.2022.11.008},
timestamp = {Sat, 29 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/gpb/ZhangBCDCSZZGZLFTL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/DelaunayH22,
author = {Maxence Delaunay and
T{\^{a}}p Ha{-}Duong},
title = {Des3PI: a fragment-based approach to design cyclic peptides targeting
protein-protein interactions},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {8},
pages = {605--621},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00468-z},
doi = {10.1007/S10822-022-00468-Z},
timestamp = {Tue, 18 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/DelaunayH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/OchoaCF22,
author = {Rodrigo Ochoa and
Pilar Cossio and
Thomas Fox},
title = {Protocol for iterative optimization of modified peptides bound to
protein targets},
journal = {J. Comput. Aided Mol. Des.},
volume = {36},
number = {11},
pages = {825--835},
year = {2022},
url = {https://doi.org/10.1007/s10822-022-00482-1},
doi = {10.1007/S10822-022-00482-1},
timestamp = {Fri, 11 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/OchoaCF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/BrankinF22,
author = {Alice E. Brankin and
Philip Fowler},
title = {Predicting antibiotic resistance in complex protein targets using
alchemical free energy methods},
journal = {J. Comput. Chem.},
volume = {43},
number = {26},
pages = {1771--1782},
year = {2022},
url = {https://doi.org/10.1002/jcc.26979},
doi = {10.1002/JCC.26979},
timestamp = {Mon, 24 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/BrankinF22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/LeeN22,
author = {Ingoo Lee and
Hojung Nam},
title = {Sequence-based prediction of protein binding regions and drug-target
interactions},
journal = {J. Cheminformatics},
volume = {14},
number = {1},
pages = {5},
year = {2022},
url = {https://doi.org/10.1186/s13321-022-00584-w},
doi = {10.1186/S13321-022-00584-W},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/LeeN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BogadoVCASP22,
author = {Mar{\'{\i}}a Lucrecia Bogado and
Roxana Noelia Villafa{\~{n}}e and
Jos{\'{e}} Leonardo G{\'{o}}mez Chavez and
Emilio Luis Angelina and
Gladis Laura Sosa and
N{\'{e}}lida Mar{\'{\i}}a Peruchena},
title = {Targeting Protein Pockets with Halogen Bonds: The Role of the Halogen
Environment},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {24},
pages = {6494--6507},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.2c00475},
doi = {10.1021/ACS.JCIM.2C00475},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/BogadoVCASP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/DelgadoWPV22,
author = {Juli{\'{a}}n A. Delgado and
Vered Wineman{-}Fisher and
Sagar Pandit and
Sameer Varma},
title = {Inclusion of High-Field Target Data in AMOEBA's Calibration Improves
Predictions of Protein-Ion Interactions},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {19},
pages = {4713--4726},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.2c00758},
doi = {10.1021/ACS.JCIM.2C00758},
timestamp = {Mon, 05 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/DelgadoWPV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LiZGW22,
author = {Wenqing Li and
Jiabin Zhang and
Li Guo and
Qiantao Wang},
title = {Importance of Three-Body Problems and Protein-Protein Interactions
in Proteolysis-Targeting Chimera Modeling: Insights from Molecular
Dynamics Simulations},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {3},
pages = {523--532},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.1c01150},
doi = {10.1021/ACS.JCIM.1C01150},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/LiZGW22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LiZXLZAZKZWYLJY22,
author = {Xiao Li and
Lun Zhang and
Jing Xu and
Chenyu Liu and
Xiaojian Zhang and
Amr Abbas Abdelmoneim and
Qian Zhang and
Jiaqi Ke and
Yingnan Zhang and
Lei Wang and
Fan Yang and
Cheng Luo and
Jia Jin and
Fei Ye},
title = {Identification, Synthesis, and Biological Evaluations of Potent Inhibitors
Targeting Type {I} Protein Arginine Methyltransferases},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {3},
pages = {692--702},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.1c01100},
doi = {10.1021/ACS.JCIM.1C01100},
timestamp = {Fri, 01 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/LiZXLZAZKZWYLJY22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/MayolDATM22,
author = {Gonzalo F. Mayol and
Lucas A. Defelipe and
Juan Pablo Arcon and
Adrian Gustavo Turjanski and
Marcelo A. Marti},
title = {Solvent Sites Improve Docking Performance of Protein-Protein Complexes
and Protein-Protein Interface-Targeted Drugs},
journal = {J. Chem. Inf. Model.},
volume = {62},
number = {15},
pages = {3577--3588},
year = {2022},
url = {https://doi.org/10.1021/acs.jcim.2c00264},
doi = {10.1021/ACS.JCIM.2C00264},
timestamp = {Thu, 22 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/MayolDATM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jei/SharmaD22,
author = {Moolchand Sharma and
Suman Deswal},
title = {DeepFNN-DTBA: prediction of drug-target binding affinity via feed-forward
neural network on drug-protein sequences},
journal = {J. Electronic Imaging},
volume = {32},
number = {5},
year = {2022},
url = {https://doi.org/10.1117/1.jei.32.5.052304},
doi = {10.1117/1.JEI.32.5.052304},
timestamp = {Mon, 12 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jei/SharmaD22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mbec/GowriR22,
author = {R. Gowri and
R. Rathipriya},
title = {Non-swarm-based computational approach for mining cancer drug target
modules in protein interaction network},
journal = {Medical Biol. Eng. Comput.},
volume = {60},
number = {7},
pages = {1947--1976},
year = {2022},
url = {https://doi.org/10.1007/s11517-022-02574-4},
doi = {10.1007/S11517-022-02574-4},
timestamp = {Sat, 13 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mbec/GowriR22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/Fang22,
author = {Hai Fang},
title = {PiER: web-based facilities tailored for genetic target prioritisation
harnessing human disease genetics, functional genomics and protein
interactions},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{W1}},
pages = {583--592},
year = {2022},
url = {https://doi.org/10.1093/nar/gkac379},
doi = {10.1093/NAR/GKAC379},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/Fang22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/netmahib/RanjanSDM22,
author = {Amit Ranjan and
Shivansh Shukla and
Deepanjan Datta and
Rajiv Misra},
title = {Generating novel molecule for target protein (SARS-CoV-2) using drug-target
interaction based on graph neural network},
journal = {Netw. Model. Anal. Health Informatics Bioinform.},
volume = {11},
number = {1},
pages = {6},
year = {2022},
url = {https://doi.org/10.1007/s13721-021-00351-1},
doi = {10.1007/S13721-021-00351-1},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/netmahib/RanjanSDM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LiuLLZ22,
author = {Ying Liu and
Ruihui Li and
Jiawei Luo and
Zhaolei Zhang},
title = {Inferring RNA-binding protein target preferences using adversarial
domain adaptation},
journal = {PLoS Comput. Biol.},
volume = {18},
number = {2},
year = {2022},
url = {https://doi.org/10.1371/journal.pcbi.1009863},
doi = {10.1371/JOURNAL.PCBI.1009863},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/LiuLLZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/symmetry/AmirochIMFN22,
author = {Siti Amiroch and
Mohammad Isa Irawan and
Imam Mukhlash and
Mohammad Hamim Zajuli Al Faroby and
Chairul Anwar Nidom},
title = {Machine Learning for the Prediction of Antiviral Compounds Targeting
Avian Influenza {A/H9N2} Viral Proteins},
journal = {Symmetry},
volume = {14},
number = {6},
pages = {1114},
year = {2022},
url = {https://doi.org/10.3390/sym14061114},
doi = {10.3390/SYM14061114},
timestamp = {Mon, 25 Jul 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/symmetry/AmirochIMFN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icml/LiuLUMJ22,
author = {Meng Liu and
Youzhi Luo and
Kanji Uchino and
Koji Maruhashi and
Shuiwang Ji},
editor = {Kamalika Chaudhuri and
Stefanie Jegelka and
Le Song and
Csaba Szepesv{\'{a}}ri and
Gang Niu and
Sivan Sabato},
title = {Generating 3D Molecules for Target Protein Binding},
booktitle = {International Conference on Machine Learning, {ICML} 2022, 17-23 July
2022, Baltimore, Maryland, {USA}},
series = {Proceedings of Machine Learning Research},
volume = {162},
pages = {13912--13924},
publisher = {{PMLR}},
year = {2022},
url = {https://proceedings.mlr.press/v162/liu22m.html},
timestamp = {Tue, 12 Jul 2022 17:36:52 +0200},
biburl = {https://dblp.org/rec/conf/icml/LiuLUMJ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwbbio/LedouxST22,
author = {Julie Ledoux and
Maxim Stolyarchuk and
Luba Tchertanov},
editor = {Ignacio Rojas and
Olga Valenzuela and
Fernando Rojas and
Luis Javier Herrera and
Francisco M. Ortu{\~{n}}o},
title = {Human Vitamin {K} Epoxide Reductase as a Target of Its Redox Protein},
booktitle = {Bioinformatics and Biomedical Engineering - 9th International Work-Conference,
{IWBBIO} 2022, Maspalomas, Gran Canaria, Spain, June 27-30, 2022,
Proceedings, Part {II}},
series = {Lecture Notes in Computer Science},
volume = {13347},
pages = {138--141},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-07802-6\_12},
doi = {10.1007/978-3-031-07802-6\_12},
timestamp = {Tue, 26 Dec 2023 17:13:20 +0100},
biburl = {https://dblp.org/rec/conf/iwbbio/LedouxST22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2204-09410,
author = {Meng Liu and
Youzhi Luo and
Kanji Uchino and
Koji Maruhashi and
Shuiwang Ji},
title = {Generating 3D Molecules for Target Protein Binding},
journal = {CoRR},
volume = {abs/2204.09410},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2204.09410},
doi = {10.48550/ARXIV.2204.09410},
eprinttype = {arXiv},
eprint = {2204.09410},
timestamp = {Mon, 25 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2204-09410.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2205-10473,
author = {Andrew D. McNaughton and
Mridula S. Bontha and
Carter R. Knutson and
Jenna A. Pope and
Neeraj Kumar},
title = {De novo design of protein target specific scaffold-based Inhibitors
via Reinforcement Learning},
journal = {CoRR},
volume = {abs/2205.10473},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2205.10473},
doi = {10.48550/ARXIV.2205.10473},
eprinttype = {arXiv},
eprint = {2205.10473},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2205-10473.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2211-11214,
author = {Haitao Lin and
Yufei Huang and
Meng Liu and
Xuanjing Li and
Shuiwang Ji and
Stan Z. Li},
title = {DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding},
journal = {CoRR},
volume = {abs/2211.11214},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2211.11214},
doi = {10.48550/ARXIV.2211.11214},
eprinttype = {arXiv},
eprint = {2211.11214},
timestamp = {Mon, 13 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2211-11214.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2211-13898,
author = {Dimitris P. Papamichail and
Madeline Febinger and
Shm Almeda and
Georgios Papamichail},
title = {Synthesis Cost-Optimal Targeted Mutant Protein Libraries},
journal = {CoRR},
volume = {abs/2211.13898},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2211.13898},
doi = {10.48550/ARXIV.2211.13898},
eprinttype = {arXiv},
eprint = {2211.13898},
timestamp = {Tue, 29 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2211-13898.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/AhammadAMATTFAS21,
author = {Foysal Ahammad and
Rahat Alam and
Rasel Mahmud and
Shahina Akhter and
Enamul Kabir Talukder and
Al Mahmud Tonmoy and
Salman Fahim and
Khalid Al{-}Ghamdi and
Abdus Samad and
Ishtiaq Qadri},
title = {Pharmacoinformatics and molecular dynamics simulation-based phytochemical
screening of neem plant (Azadiractha indica) against human cancer
by targeting {MCM7} protein},
journal = {Briefings Bioinform.},
volume = {22},
number = {5},
year = {2021},
url = {https://doi.org/10.1093/bib/bbab098},
doi = {10.1093/BIB/BBAB098},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/AhammadAMATTFAS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/BaiTXLHY21,
author = {Qifeng Bai and
Shuoyan Tan and
Tingyang Xu and
Huanxiang Liu and
Junzhou Huang and
Xiaojun Yao},
title = {MolAICal: a soft tool for 3D drug design of protein targets by artificial
intelligence and classical algorithm},
journal = {Briefings Bioinform.},
volume = {22},
number = {3},
year = {2021},
url = {https://doi.org/10.1093/bib/bbaa161},
doi = {10.1093/BIB/BBAA161},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/BaiTXLHY21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KhanK21,
author = {Abdul Arif Khan and
Zakir Khan},
title = {Comparative host-pathogen protein-protein interaction analysis of
recent coronavirus outbreaks and important host targets identification},
journal = {Briefings Bioinform.},
volume = {22},
number = {2},
pages = {1206--1214},
year = {2021},
url = {https://doi.org/10.1093/bib/bbaa207},
doi = {10.1093/BIB/BBAA207},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KhanK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LoaizaDLK21,
author = {Cristian D. Loaiza and
Naveen Duhan and
Matthew Lister and
Rakesh Kaundal},
title = {In silico prediction of host-pathogen protein interactions in melioidosis
pathogen Burkholderia pseudomallei and human reveals novel virulence
factors and their targets},
journal = {Briefings Bioinform.},
volume = {22},
number = {3},
year = {2021},
url = {https://doi.org/10.1093/bib/bbz162},
doi = {10.1093/BIB/BBZ162},
timestamp = {Sat, 31 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LoaizaDLK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biosystems/DAcunto21,
author = {Mario D'Acunto},
title = {Protein-DNA target search relies on quantum walk},
journal = {Biosyst.},
volume = {201},
pages = {104340},
year = {2021},
url = {https://doi.org/10.1016/j.biosystems.2020.104340},
doi = {10.1016/J.BIOSYSTEMS.2020.104340},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biosystems/DAcunto21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/Follis21,
author = {Ariele Viacava Follis},
title = {Centrality of drug targets in protein networks},
journal = {{BMC} Bioinform.},
volume = {22},
number = {3},
pages = {527},
year = {2021},
url = {https://doi.org/10.1186/s12859-021-04342-x},
doi = {10.1186/S12859-021-04342-X},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/Follis21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/AkyolK21,
author = {Kubra Akyol and
Deryanur Kilic},
title = {Discovery of novel and selective inhibitors targeting protein tyrosine
phosphatase 1B {(PTP1B):} Virtual screening and molecular dynamic
simulation},
journal = {Comput. Biol. Medicine},
volume = {139},
pages = {104959},
year = {2021},
url = {https://doi.org/10.1016/j.compbiomed.2021.104959},
doi = {10.1016/J.COMPBIOMED.2021.104959},
timestamp = {Tue, 08 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cbm/AkyolK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/ErukainureAMRAK21,
author = {Ochuko L. Erukainure and
Olubunmi Atolani and
Aliyu Muhammad and
Rahul Ravichandran and
Musa M. Abarshi and
Sanusi B. Katsayal and
Chika I. Chukwuma and
Robert Preissner and
Priyanka Banerjee and
M. Ahmed Mesaik},
title = {Translational suppression of {SARS-COV-2} {ORF8} protein mRNA as a
Viable therapeutic target against {COVID-19:} Computational studies
on potential roles of isolated compounds from \emph{Clerodendrum volubile}
leaves},
journal = {Comput. Biol. Medicine},
volume = {139},
pages = {104964},
year = {2021},
url = {https://doi.org/10.1016/j.compbiomed.2021.104964},
doi = {10.1016/J.COMPBIOMED.2021.104964},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/ErukainureAMRAK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/GarciaHKAWPTDVH21,
author = {Rolando Garc{\'{\i}}a and
Anas Hussain and
Prasad Koduru and
Murat Atis and
Kathleen Wilson and
Jason Y. Park and
Inimary T. Toby and
Kimberly Diwa and
Lavang Vu and
Samuel Ho and
Fajar Adnan and
Ashley Nguyen and
Andrew Cox and
Timothy Kirtek and
Patricia Garc{\'{\i}}a and
Yanhui Li and
Heather Jones and
Guanglu Shi and
Allen Green and
David Rosenbaum},
title = {Identification of potential antiviral compounds against SARS-CoV-2
structural and non structural protein targets: {A} pharmacoinformatics
study of the {CAS} {COVID-19} dataset},
journal = {Comput. Biol. Medicine},
volume = {133},
pages = {104364},
year = {2021},
url = {https://doi.org/10.1016/j.compbiomed.2021.104364},
doi = {10.1016/J.COMPBIOMED.2021.104364},
timestamp = {Fri, 08 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cbm/GarciaHKAWPTDVH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/MishraBPAAT21,
author = {Ganesh Prasad Mishra and
Rajendra N. Bhadane and
Debadash Panigrahi and
Haneen A. Amawi and
Charles R. Asbhy Jr. and
Amit K. Tiwari},
title = {The interaction of the bioflavonoids with five SARS-CoV-2 proteins
targets: An i\emph{n silico} study},
journal = {Comput. Biol. Medicine},
volume = {134},
pages = {104464},
year = {2021},
url = {https://doi.org/10.1016/j.compbiomed.2021.104464},
doi = {10.1016/J.COMPBIOMED.2021.104464},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/MishraBPAAT21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/SkariyachanGMUN21,
author = {Sinosh Skariyachan and
Dharshini Gopal and
Aditi G. Muddebihalkar and
Akshay Uttarkar and
Vidya Niranjan},
title = {Structural insights on the interaction potential of natural leads
against major protein targets of SARS-CoV-2: Molecular modelling,
docking and dynamic simulation studies},
journal = {Comput. Biol. Medicine},
volume = {132},
pages = {104325},
year = {2021},
url = {https://doi.org/10.1016/j.compbiomed.2021.104325},
doi = {10.1016/J.COMPBIOMED.2021.104325},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/SkariyachanGMUN21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijaip/SahaPCBN21,
author = {Sovan Saha and
Abhimanyu Prasad and
Piyali Chatterjee and
Subhadip Basu and
Mita Nasipuri},
title = {\emph{Modified FPred-Apriori}: improving function prediction of target
proteins from essential neighbours by finding their association with
relevant functional groups using Apriori algorithm},
journal = {Int. J. Adv. Intell. Paradigms},
volume = {19},
number = {1},
pages = {61--83},
year = {2021},
url = {https://doi.org/10.1504/IJAIP.2021.114582},
doi = {10.1504/IJAIP.2021.114582},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ijaip/SahaPCBN21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijis/LiLYLGW21,
author = {Yang Li and
Xiaozhang Liu and
Zhu{-}Hong You and
Li{-}Ping Li and
Jian{-}Xin Guo and
Zheng Wang},
title = {A computational approach for predicting drug-target interactions from
protein sequence and drug substructure fingerprint information},
journal = {Int. J. Intell. Syst.},
volume = {36},
number = {1},
pages = {593--609},
year = {2021},
url = {https://doi.org/10.1002/int.22332},
doi = {10.1002/INT.22332},
timestamp = {Tue, 14 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ijis/LiLYLGW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/Sixto-LopezM21,
author = {Yudibeth Sixto{-}L{\'{o}}pez and
Marlet Mart{\'{\i}}nez{-}Archundia},
title = {Drug repositioning to target {NSP15} protein on SARS-CoV-2 as possible
{COVID-19} treatment},
journal = {J. Comput. Chem.},
volume = {42},
number = {13},
pages = {897--907},
year = {2021},
url = {https://doi.org/10.1002/jcc.26512},
doi = {10.1002/JCC.26512},
timestamp = {Fri, 17 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcc/Sixto-LopezM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FreidelA21,
author = {Matthew R. Freidel and
Roger S. Armen},
title = {Modeling the Structure-Activity Relationship of Arbidol Derivatives
and Other SARS-CoV-2 Fusion Inhibitors Targeting the {S2} Segment
of the Spike Protein},
journal = {J. Chem. Inf. Model.},
volume = {61},
number = {12},
pages = {5906--5922},
year = {2021},
url = {https://doi.org/10.1021/acs.jcim.1c01061},
doi = {10.1021/ACS.JCIM.1C01061},
timestamp = {Fri, 21 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/FreidelA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/HuRZZY21,
author = {Jun Hu and
Liang Rao and
Yi{-}Heng Zhu and
Gui{-}Jun Zhang and
Dong{-}Jun Yu},
title = {TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins
via Weighted Convolutional Features},
journal = {J. Chem. Inf. Model.},
volume = {61},
number = {1},
pages = {505--515},
year = {2021},
url = {https://doi.org/10.1021/acs.jcim.0c00735},
doi = {10.1021/ACS.JCIM.0C00735},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/HuRZZY21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/KimCK21,
author = {Dong{-}Gun Kim and
Yoonjoo Choi and
Hak{-}Sung Kim},
title = {Epitopes of Protein Binders Are Related to the Structural Flexibility
of a Target Protein Surface},
journal = {J. Chem. Inf. Model.},
volume = {61},
number = {4},
pages = {2099--2107},
year = {2021},
url = {https://doi.org/10.1021/acs.jcim.0c01397},
doi = {10.1021/ACS.JCIM.0C01397},
timestamp = {Sun, 16 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/KimCK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/Nunes-AlvesOW21,
author = {Ariane Nunes{-}Alves and
Fabian Ormersbach and
Rebecca C. Wade},
title = {Prediction of the Drug-Target Binding Kinetics for Flexible Proteins
by Comparative Binding Energy Analysis},
journal = {J. Chem. Inf. Model.},
volume = {61},
number = {7},
pages = {3708--3721},
year = {2021},
url = {https://doi.org/10.1021/acs.jcim.1c00639},
doi = {10.1021/ACS.JCIM.1C00639},
timestamp = {Thu, 16 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/Nunes-AlvesOW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/netmahib/UdofiaGOOI21,
author = {Inemesit A. Udofia and
Kofoworola O. Gbayo and
Oluwakemi A. Oloba{-}Whenu and
Taofeek B. Ogunbayo and
Chukwuemeka Isanbor},
title = {In silico studies of selected multi-drug targeting against 3CLpro
and nsp12 RNA-dependent RNA-polymerase proteins of SARS-CoV-2 and
SARS-CoV},
journal = {Netw. Model. Anal. Health Informatics Bioinform.},
volume = {10},
number = {1},
pages = {22},
year = {2021},
url = {https://doi.org/10.1007/s13721-021-00299-2},
doi = {10.1007/S13721-021-00299-2},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/netmahib/UdofiaGOOI21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/DoganGBKABMC21,
author = {Tunca Dogan and
Ece Akhan G{\"{u}}zelcan and
Marcus Baumann and
Altay Koyas and
Heval Atas and
Ian R. Baxendale and
Maria Jesus Martin and
Reng{\"{u}}l {\c{C}}etin{-}Atalay},
title = {Protein domain-based prediction of drug/compound-target interactions
and experimental validation on {LIM} kinases},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {11},
year = {2021},
url = {https://doi.org/10.1371/journal.pcbi.1009171},
doi = {10.1371/JOURNAL.PCBI.1009171},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/DoganGBKABMC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LichtingerGCR21,
author = {Simon M. Lichtinger and
Adiran Garaizar and
Rosana Collepardo{-}Guevara and
Aleks Reinhardt},
title = {Targeted modulation of protein liquid-liquid phase separation by evolution
of amino-acid sequence},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {8},
year = {2021},
url = {https://doi.org/10.1371/journal.pcbi.1009328},
doi = {10.1371/JOURNAL.PCBI.1009328},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/LichtingerGCR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/Schneider-Lunitz21,
author = {Valentin Schneider{-}Lunitz and
Jorge Ruiz{-}Orera and
Norbert H{\"{u}}bner and
Sebastiaan van Heesch},
title = {Multifunctional RNA-binding proteins influence mRNA abundance and
translational efficiency of distinct sets of target genes},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {12},
year = {2021},
url = {https://doi.org/10.1371/journal.pcbi.1009658},
doi = {10.1371/JOURNAL.PCBI.1009658},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/Schneider-Lunitz21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bigdataconf/ChenYGSB21,
author = {Serena H. Chen and
M. Todd Young and
John Gounley and
Christopher B. Stanley and
Debsindhu Bhowmik},
editor = {Yixin Chen and
Heiko Ludwig and
Yicheng Tu and
Usama M. Fayyad and
Xingquan Zhu and
Xiaohua Hu and
Suren Byna and
Xiong Liu and
Jianping Zhang and
Shirui Pan and
Vagelis Papalexakis and
Jianwu Wang and
Alfredo Cuzzocrea and
Carlos Ordonez},
title = {How Distinct Structural Flexibility within SARS-CoV-2 Spike Protein
Reveals Potential Therapeutic Targets},
booktitle = {2021 {IEEE} International Conference on Big Data (Big Data), Orlando,
FL, USA, December 15-18, 2021},
pages = {4333--4341},
publisher = {{IEEE}},
year = {2021},
url = {https://doi.org/10.1109/BigData52589.2021.9671323},
doi = {10.1109/BIGDATA52589.2021.9671323},
timestamp = {Fri, 28 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bigdataconf/ChenYGSB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cibcb/KosugiO21,
author = {Takatsugi Kosugi and
Masahito Ohue},
editor = {Jennifer Hallinan and
Madhu Chetty and
Gonzalo Ruz Heredia and
Adrian Shatte and
Suryani Lim},
title = {Quantitative Estimate of Protein-Protein Interaction Targeting Drug-likeness},
booktitle = {{IEEE} Conference on Computational Intelligence in Bioinformatics
and Computational Biology, {CIBCB} 2021, Melbourne, Australia, October
13-15, 2021},
pages = {1--8},
publisher = {{IEEE}},
year = {2021},
url = {https://doi.org/10.1109/CIBCB49929.2021.9562931},
doi = {10.1109/CIBCB49929.2021.9562931},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cibcb/KosugiO21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icic/YanYWC21,
author = {Xin Yan and
Zhu{-}Hong You and
Lei Wang and
Peng{-}Peng Chen},
editor = {De{-}Shuang Huang and
Kang{-}Hyun Jo and
Jianqiang Li and
Valeriya V. Gribova and
Prashan Premaratne},
title = {{CNNEMS:} Using Convolutional Neural Networks to Predict Drug-Target
Interactions by Combining Protein Evolution and Molecular Structures
Information},
booktitle = {Intelligent Computing Theories and Application - 17th International
Conference, {ICIC} 2021, Shenzhen, China, August 12-15, 2021, Proceedings,
Part {III}},
series = {Lecture Notes in Computer Science},
volume = {12838},
pages = {570--579},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-84532-2\_51},
doi = {10.1007/978-3-030-84532-2\_51},
timestamp = {Mon, 16 Aug 2021 16:01:13 +0200},
biburl = {https://dblp.org/rec/conf/icic/YanYWC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sc/StevensonJKBBBB21,
author = {Garrett A. Stevenson and
Derek Jones and
Hyojin Kim and
W. F. Drew Bennett and
Brian J. Bennion and
Monica Borucki and
Feliza Bourguet and
Aidan Epstein and
Magdalena Franco and
Brooke Harmon and
Stewart He and
Max P. Katz and
Daniel A. Kirshner and
Victoria Lao and
Edmond Y. Lau and
Jacky Lo and
Kevin McLoughlin and
Richard Mosesso and
Deepa K. Murugesh and
Oscar A. Negrete and
Edwin A. Saada and
Brent Segelke and
Maxwell Stefan and
Marisa W. Torres and
Dina Weilhammer and
Sergio Ernesto Wong and
Yue Yang and
Adam T. Zemla and
Xiaohua Zhang and
Fangqiang Zhu and
Felice C. Lightstone and
Jonathan E. Allen},
editor = {Bronis R. de Supinski and
Mary W. Hall and
Todd Gamblin},
title = {High-throughput virtual screening of small molecule inhibitors for
SARS-CoV-2 protein targets with deep fusion models},
booktitle = {International Conference for High Performance Computing, Networking,
Storage and Analysis, {SC} 2021, St. Louis, Missouri, USA, November
14-19, 2021},
pages = {74},
publisher = {{ACM}},
year = {2021},
url = {https://doi.org/10.1145/3458817.3476193},
doi = {10.1145/3458817.3476193},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sc/StevensonJKBBBB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2104-04547,
author = {Garrett A. Stevenson and
Derek Jones and
Hyojin Kim and
W. F. Drew Bennett and
Brian J. Bennion and
Monica Borucki and
Feliza Bourguet and
Aidan Epstein and
Magdalena Franco and
Brooke Harmon and
Stewart He and
Max P. Katz and
Daniel A. Kirshner and
Victoria Lao and
Edmond Y. Lau and
Jacky Lo and
Kevin McLoughlin and
Richard Mosesso and
Deepa K. Murugesh and
Oscar A. Negrete and
Edwin A. Saada and
Brent Segelke and
Maxwell Stefan and
Marisa W. Torres and
Dina Weilhammer and
Sergio Ernesto Wong and
Yue Yang and
Adam T. Zemla and
Xiaohua Zhang and
Fangqiang Zhu and
Felice C. Lightstone and
Jonathan E. Allen},
title = {High-Throughput Virtual Screening of Small Molecule Inhibitors for
SARS-CoV-2 Protein Targets with Deep Fusion Models},
journal = {CoRR},
volume = {abs/2104.04547},
year = {2021},
url = {https://arxiv.org/abs/2104.04547},
eprinttype = {arXiv},
eprint = {2104.04547},
timestamp = {Thu, 31 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2104-04547.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2112-13168,
author = {Ayan Chatterjee and
Omair Shafi Ahmed and
Robin Walters and
Zohair Shafi and
Deisy Morselli Gysi and
Rose Yu and
Tina Eliassi{-}Rad and
Albert{-}L{\'{a}}szl{\'{o}} Barab{\'{a}}si and
Giulia Menichetti},
title = {AI-Bind: Improving Binding Predictions for Novel Protein Targets and
Ligands},
journal = {CoRR},
volume = {abs/2112.13168},
year = {2021},
url = {https://arxiv.org/abs/2112.13168},
eprinttype = {arXiv},
eprint = {2112.13168},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2112-13168.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/tr/Rifaioglu20,
author = {Ahmet S{\"{u}}reyya Rifaioglu},
title = {Deep learning for prediction of drug-target interaction space and
protein functions ({\.{I}}la{\c{c}}-hedef protein etkile{\c{s}}im
uzay{\i} ve protein fonksiyonlar{\i}n{\i}n tahmini i{\c{c}}in derin
{\"{o}}{\u{g}}renme)},
school = {Middle East Technical University, Turkey},
year = {2020},
url = {https://tez.yok.gov.tr/UlusalTezMerkezi/tezDetay.jsp?id=aiweQO9htoM\_cuLf6aF5CQ\&no=Dl\_XvbJc-glvFkkJuHFv9A},
timestamp = {Sun, 03 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/phd/tr/Rifaioglu20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/access/ZhanYCLYPK20,
author = {Xinke Zhan and
Zhu{-}Hong You and
Jinfan Cai and
Liping Li and
Changqing Yu and
Jie Pan and
Jiangkun Kong},
title = {Prediction of Drug-Target Interactions by Ensemble Learning Method
From Protein Sequence and Drug Fingerprint},
journal = {{IEEE} Access},
volume = {8},
pages = {185465--185476},
year = {2020},
url = {https://doi.org/10.1109/ACCESS.2020.3026479},
doi = {10.1109/ACCESS.2020.3026479},
timestamp = {Thu, 11 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/access/ZhanYCLYPK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChaputGSDV20,
author = {Ludovic Chaput and
Valentin Guillaume and
Natesh Singh and
Benoit Deprez and
Bruno O. Villoutreix},
title = {FastTargetPred: a program enabling the fast prediction of putative
protein targets for input chemical databases},
journal = {Bioinform.},
volume = {36},
number = {14},
pages = {4225--4226},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa494},
doi = {10.1093/BIOINFORMATICS/BTAA494},
timestamp = {Fri, 25 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChaputGSDV20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MohamedNN20,
author = {Sameh K. Mohamed and
V{\'{\i}}t Nov{\'{a}}cek and
Aayah Nounu},
title = {Discovering protein drug targets using knowledge graph embeddings},
journal = {Bioinform.},
volume = {36},
number = {2},
pages = {603--610},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btz600},
doi = {10.1093/BIOINFORMATICS/BTZ600},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MohamedNN20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DezsoC20,
author = {Zolt{\'{a}}n Dezs{\"{o}} and
Michele Ceccarelli},
title = {Machine learning prediction of oncology drug targets based on protein
and network properties},
journal = {{BMC} Bioinform.},
volume = {21},
number = {1},
pages = {104},
year = {2020},
url = {https://doi.org/10.1186/s12859-020-3442-9},
doi = {10.1186/S12859-020-3442-9},
timestamp = {Tue, 16 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/DezsoC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/PitsillouLHK20,
author = {Eleni Pitsillou and
Julia Liang and
Andrew Hung and
Tom C. Karagiannis},
title = {Molecular docking utilising the OliveNet{\texttrademark} library reveals
novel phenolic compounds which may potentially target key proteins
associated with major depressive disorder},
journal = {Comput. Biol. Chem.},
volume = {86},
pages = {107234},
year = {2020},
url = {https://doi.org/10.1016/j.compbiolchem.2020.107234},
doi = {10.1016/J.COMPBIOLCHEM.2020.107234},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/candc/PitsillouLHK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijcbdd/AlamRHC20,
author = {Rafat Alam and
G. M. Sayedur Rahman and
Nahid Hasan and
Abu Sayeed Chowdhury},
title = {A De-Novo drug design and {ADMET} study to design small molecule stabilisers
targeting mutant {(V210I)} human prion protein against familial Creutzfeldt-Jakob
disease (fCJD)},
journal = {Int. J. Comput. Biol. Drug Des.},
volume = {13},
number = {1},
pages = {21--35},
year = {2020},
url = {https://doi.org/10.1504/IJCBDD.2020.105103},
doi = {10.1504/IJCBDD.2020.105103},
timestamp = {Thu, 07 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijcbdd/AlamRHC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/BelgamoAPRRTCF20,
author = {Juli{\'{a}}n A. B{\'{e}}lgamo and
Lucas N. Alberca and
Jorge L. P{\'{o}}rfido and
Franco N. Caram Romero and
Santiago Rodriguez and
Alan Talevi and
Betina C{\'{o}}rsico and
Gisela R. Franchini},
title = {Application of target repositioning and in silico screening to exploit
fatty acid binding proteins (FABPs) from Echinococcus multilocularis
as possible drug targets},
journal = {J. Comput. Aided Mol. Des.},
volume = {34},
number = {12},
pages = {1275--1288},
year = {2020},
url = {https://doi.org/10.1007/s10822-020-00352-8},
doi = {10.1007/S10822-020-00352-8},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/BelgamoAPRRTCF20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/DrummondHLW20,
author = {Michael L. Drummond and
Andrew Henry and
Huifang Li and
Christopher I. Williams},
title = {Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation
and Targeted Protein Degradation via New In Silico Methodologies},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {10},
pages = {5234--5254},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.0c00897},
doi = {10.1021/ACS.JCIM.0C00897},
timestamp = {Wed, 01 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/DrummondHLW20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/KumarSSKJPDKKPR20,
author = {Sumit Kumar and
Prem Prakash Sharma and
Uma Shankar and
Dhruva Kumar and
Sanjeev K. Joshi and
Lindomar Pena and
Ravi Durvasula and
Amit Kumar and
Prakasha Kempaiah and
Poonam and
Brijesh Rathi},
title = {Discovery of New Hydroxyethylamine Analogs against 3CLpro Protein
Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation,
and Structure-Activity Relationship Studies},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {12},
pages = {5754--5770},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.0c00326},
doi = {10.1021/ACS.JCIM.0C00326},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/KumarSSKJPDKKPR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LiMG20,
author = {Jianyu Li and
Aur{\'{e}}lien F. A. Moumbock and
Stefan G{\"{u}}nther},
title = {Exploring Cocrystallized Aromatic Cage Binders to Target Histone Methylation
Reader Proteins},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {10},
pages = {5225--5233},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.0c00765},
doi = {10.1021/ACS.JCIM.0C00765},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/LiMG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/PinziR20,
author = {Luca Pinzi and
Giulio Rastelli},
title = {Identification of Target Associations for Polypharmacology from Analysis
of Crystallographic Ligands of the Protein Data Bank},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {1},
pages = {372--390},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.9b00821},
doi = {10.1021/ACS.JCIM.9B00821},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/PinziR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/YangKBPYLS20,
author = {Jinsol Yang and
Sohee Kwon and
Sang{-}Hun Bae and
Kyoung Mii Park and
Changsik Yoon and
Ji{-}Hyun Lee and
Chaok Seok},
title = {GalaxySagittarius: Structure- and Similarity-Based Prediction of Protein
Targets for Druglike Compounds},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {6},
pages = {3246--3254},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.0c00104},
doi = {10.1021/ACS.JCIM.0C00104},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/YangKBPYLS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/ZhangWWLZPW20,
author = {Xiaozheng Zhang and
Yibo Wang and
Hongshuang Wang and
Hongyuan Li and
Tianshu Zhang and
Yinghua Peng and
Xiaohui Wang},
title = {Exploring Methamphetamine Nonenantioselectively Targeting Toll-like
Receptor 4/Myeloid Differentiation Protein 2 by in Silico Simulations
and Wet-Lab Techniques},
journal = {J. Chem. Inf. Model.},
volume = {60},
number = {3},
pages = {1607--1613},
year = {2020},
url = {https://doi.org/10.1021/acs.jcim.9b01040},
doi = {10.1021/ACS.JCIM.9B01040},
timestamp = {Fri, 17 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/ZhangWWLZPW20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/midm/ZhengMZCX20a,
author = {Yuyu Zheng and
Xiangyu Meng and
Pierre Zweigenbaum and
Lingling Chen and
Jingbo Xia},
title = {Hybrid phenotype mining method for investigating off-target protein
and underlying side effects of anti-tumor immunotherapy},
journal = {{BMC} Medical Informatics Decis. Mak.},
volume = {20-S},
number = {3},
pages = {133},
year = {2020},
url = {https://doi.org/10.1186/s12911-020-1105-4},
doi = {10.1186/S12911-020-1105-4},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/midm/ZhengMZCX20a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BouvretteBBL20,
author = {Louis Philip Benoit Bouvrette and
Samantha Bovaird and
Mathieu Blanchette and
Eric L{\'{e}}cuyer},
title = {oRNAment: a database of putative {RNA} binding protein target sites
in the transcriptomes of model species},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D166--D173},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz986},
doi = {10.1093/NAR/GKZ986},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/BouvretteBBL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/netmahib/DabadeMBT20,
author = {Sapna Jain Dabade and
Dheeraj Mandloi and
Amritlal V. Bajaj and
Abhilash Thakur},
title = {In silico evaluation of inhibitory potential of novel triazole derivatives
against therapeutic target myristoyl-CoA: protein N-myristoyltransferase
{(NMT)} of Candida albicans},
journal = {Netw. Model. Anal. Health Informatics Bioinform.},
volume = {9},
number = {1},
pages = {60},
year = {2020},
url = {https://doi.org/10.1007/s13721-020-00265-4},
doi = {10.1007/S13721-020-00265-4},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/netmahib/DabadeMBT20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/soco/Lopez-CamachoGG20,
author = {Esteban L{\'{o}}pez{-}Camacho and
Mar{\'{\i}}a Jes{\'{u}}s Garc{\'{\i}}a{-}Godoy and
Jos{\'{e}} Garc{\'{\i}}a{-}Nieto and
Antonio J. Nebro and
Jos{\'{e}} Francisco Aldana Montes},
title = {Optimizing ligand conformations in flexible protein targets: a multi-objective
strategy},
journal = {Soft Comput.},
volume = {24},
number = {14},
pages = {10705--10719},
year = {2020},
url = {https://doi.org/10.1007/s00500-019-04575-2},
doi = {10.1007/S00500-019-04575-2},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/soco/Lopez-CamachoGG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/soco/NarmadhaP20,
author = {D. Narmadha and
Albert Pravin},
title = {An intelligent computer-aided approach for target protein prediction
in infectious diseases},
journal = {Soft Comput.},
volume = {24},
number = {19},
pages = {14707--14720},
year = {2020},
url = {https://doi.org/10.1007/s00500-020-04815-w},
doi = {10.1007/S00500-020-04815-W},
timestamp = {Thu, 23 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/soco/NarmadhaP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/HuZZYZ20,
author = {Jun Hu and
Xiaogen Zhou and
Yi{-}Heng Zhu and
Dong{-}Jun Yu and
Gui{-}Jun Zhang},
title = {TargetDBP: Accurate DNA-Binding Protein Prediction Via Sequence-Based
Multi-View Feature Learning},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {17},
number = {4},
pages = {1419--1429},
year = {2020},
url = {https://doi.org/10.1109/TCBB.2019.2893634},
doi = {10.1109/TCBB.2019.2893634},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/HuZZYZ20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LeeH20,
author = {Wook Lee and
Kyungsook Han},
title = {Constructive Prediction of Potential {RNA} Aptamers for a Protein
Target},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {17},
number = {5},
pages = {1476--1482},
year = {2020},
url = {https://doi.org/10.1109/TCBB.2019.2951114},
doi = {10.1109/TCBB.2019.2951114},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/LeeH20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icic/YanYWLZW20,
author = {Xin Yan and
Zhu{-}Hong You and
Lei Wang and
Li{-}Ping Li and
Kai Zheng and
Mei{-}Neng Wang},
editor = {De{-}Shuang Huang and
Kang{-}Hyun Jo},
title = {{DTIFS:} {A} Novel Computational Approach for Predicting Drug-Target
Interactions from Drug Structure and Protein Sequence},
booktitle = {Intelligent Computing Theories and Application - 16th International
Conference, {ICIC} 2020, Bari, Italy, October 2-5, 2020, Proceedings,
Part {II}},
series = {Lecture Notes in Computer Science},
volume = {12464},
pages = {371--383},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-60802-6\_33},
doi = {10.1007/978-3-030-60802-6\_33},
timestamp = {Wed, 03 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icic/YanYWLZW20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/StanleyGSASD20,
author = {Jacob T. Stanley and
Alison R. Gilchrist and
Alex C. Stabell and
Mary A. Allen and
Sara L. Sawyer and
Robin D. Dowell},
title = {Two-stage {ML} Classifier for Identifying Host Protein Targets of
the Dengue Protease},
booktitle = {Pacific Symposium on Biocomputing 2020, Fairmont Orchid, Hawaii, USA,
January 3-7, 2020},
pages = {487--498},
year = {2020},
url = {https://psb.stanford.edu/psb-online/proceedings/psb20/Stanley.pdf},
timestamp = {Fri, 13 Aug 2021 16:31:26 +0200},
biburl = {https://dblp.org/rec/conf/psb/StanleyGSASD20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:series/mimb/Ivanov20,
author = {Andrey A. Ivanov},
editor = {Stefan Canzar and
Francisca Rojas Ringeling},
title = {Explore Protein-Protein Interactions for Cancer Target Discovery Using
the OncoPPi Portal},
booktitle = {Protein-Protein Interaction Networks, Methods and Protocols},
series = {Methods in Molecular Biology},
volume = {2074},
pages = {145--164},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-1-4939-9873-9\_12},
doi = {10.1007/978-1-4939-9873-9\_12},
timestamp = {Tue, 07 May 2024 20:28:21 +0200},
biburl = {https://dblp.org/rec/series/mimb/Ivanov20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2007-12073,
author = {Seongyong Park and
Shujaat Khan and
Abdul Wahab},
title = {E3-targetPred: Prediction of E3-Target Proteins Using Deep Latent
Space Encoding},
journal = {CoRR},
volume = {abs/2007.12073},
year = {2020},
url = {https://arxiv.org/abs/2007.12073},
eprinttype = {arXiv},
eprint = {2007.12073},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2007-12073.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/basesearch/Masera19,
author = {Luca Masera},
title = {Multi-target Prediction Methods for Bioinformatics: Approaches for
Protein Function Prediction and Candidate Discovery for Gene Regulatory
Network Expansion},
school = {University of Trento, Italy},
year = {2019},
url = {http://eprints-phd.biblio.unitn.it/3764/},
timestamp = {Tue, 02 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/phd/basesearch/Masera19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/hal/Rao19,
author = {Rajas Mallenahalli Rao},
title = {Study of structural and functional dynamics of translocator protein,
a new target for treatment of malaria. ({\'{E}}tude de la dynamique
structurale et fonctionnelle de la prot{\'{e}}ine translocatrice,
une nouvelle cible pour traiter le paludisme)},
school = {University of La R{\'{e}}union, Saint-Denis, France},
year = {2019},
url = {https://tel.archives-ouvertes.fr/tel-02477321},
timestamp = {Tue, 21 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/phd/hal/Rao19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/tr/Ozturk19,
author = {Hakime {\"{O}}zt{\"{u}}rk},
title = {Text-based machine learning methodologies for modelling drug-target
interactions (Protein-ila{\c{c}} etkile{\c{s}}imlerinin metin tabanl{\i}
makine {\"{o}}{\u{g}}renmesi y{\"{o}}ntemleri ile modellenmesi)},
school = {Bo{\u{g}}azi{\c{c}}i University, Turkey},
year = {2019},
url = {https://tez.yok.gov.tr/UlusalTezMerkezi/tezDetay.jsp?id=QNRp3jG7-uYiVb2DDpdVNQ\&no=n4RhsoNi7d\_X682WeC98Lw},
timestamp = {Sun, 03 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/phd/tr/Ozturk19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/abi/MustafaBG19,
author = {Sabeena Mustafa and
Hanan Balkhy and
Musa Gabere},
title = {Peptide-Protein Interaction Studies of Antimicrobial Peptides Targeting
Middle East Respiratory Syndrome Coronavirus Spike Protein: An In
Silico Approach},
journal = {Adv. Bioinformatics},
volume = {2019},
pages = {6815105:1--6815105:16},
year = {2019},
url = {https://doi.org/10.1155/2019/6815105},
doi = {10.1155/2019/6815105},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/abi/MustafaBG19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/access/MahmudCJLSA19,
author = {S. M. Hasan Mahmud and
Wenyu Chen and
Hosney Jahan and
Yongsheng Liu and
Nasir Islam Sujan and
Saeed Ahmed},
title = {iDTi-CSsmoteB: Identification of Drug-Target Interaction Based on
Drug Chemical Structure and Protein Sequence Using XGBoost With Over-Sampling
Technique {SMOTE}},
journal = {{IEEE} Access},
volume = {7},
pages = {48699--48714},
year = {2019},
url = {https://doi.org/10.1109/ACCESS.2019.2910277},
doi = {10.1109/ACCESS.2019.2910277},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/access/MahmudCJLSA19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuLCWPHYKZ19,
author = {Jiansheng Wu and
Ben Liu and
Wallace K. B. Chan and
Weijian Wu and
Tao Pang and
Haifeng Hu and
Shancheng Yan and
Xiaoyan Ke and
Yang Zhang},
title = {Precise modelling and interpretation of bioactivities of ligands targeting
{G} protein-coupled receptors},
journal = {Bioinform.},
volume = {35},
number = {14},
pages = {i324--i332},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/btz336},
doi = {10.1093/BIOINFORMATICS/BTZ336},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuLCWPHYKZ19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AckermanAHS19,
author = {Emily E. Ackerman and
John F. Alcorn and
Takeshi Hase and
Jason E. Shoemaker},
title = {A dual controllability analysis of influenza virus-host protein-protein
interaction networks for antiviral drug target discovery},
journal = {{BMC} Bioinform.},
volume = {20},
number = {1},
pages = {297:1--297:13},
year = {2019},
url = {https://doi.org/10.1186/s12859-019-2917-z},
doi = {10.1186/S12859-019-2917-Z},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AckermanAHS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HuZCGZW19,
author = {ShanShan Hu and
Chenglin Zhang and
Peng Chen and
Pengying Gu and
Jun Zhang and
Bing Wang},
title = {Predicting drug-target interactions from drug structure and protein
sequence using novel convolutional neural networks},
journal = {{BMC} Bioinform.},
volume = {20-S},
number = {25},
pages = {689},
year = {2019},
url = {https://doi.org/10.1186/s12859-019-3263-x},
doi = {10.1186/S12859-019-3263-X},
timestamp = {Thu, 15 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HuZCGZW19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PercontiRCBBTFG19,
author = {Giovanni Perconti and
Patrizia Rubino and
Flavia Contino and
Serena Bivona and
Giorgio Bertolazzi and
Michele Tumminello and
Salvatore Feo and
Agata Giallongo and
Claudia Coronnello},
title = {RIP-Chip analysis supports different roles for {AGO2} and {GW182}
proteins in recruiting and processing microRNA targets},
journal = {{BMC} Bioinform.},
volume = {20-S},
number = {4},
pages = {120:1--120:13},
year = {2019},
url = {https://doi.org/10.1186/s12859-019-2683-y},
doi = {10.1186/S12859-019-2683-Y},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/PercontiRCBBTFG19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/AhamadIADH19,
author = {Shahzaib Ahamad and
Asimul Islam and
Faizan Ahmad and
Neeraj Dwivedi and
Md. Imtaiyaz Hassan},
title = {2/3D-QSAR, molecular docking and {MD} simulation studies of \emph{FtsZ}
protein targeting benzimidazoles derivatives},
journal = {Comput. Biol. Chem.},
volume = {78},
pages = {398--413},
year = {2019},
url = {https://doi.org/10.1016/j.compbiolchem.2018.12.017},
doi = {10.1016/J.COMPBIOLCHEM.2018.12.017},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/AhamadIADH19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/AllenMMB19,
author = {Chad H. G. Allen and
Lewis H. Mervin and
Samar Y. Mahmoud and
Andreas Bender},
title = {Leveraging heterogeneous data from {GHS} toxicity annotations, molecular
and protein target descriptors and Tox21 assay readouts to predict
and rationalise acute toxicity},
journal = {J. Cheminformatics},
volume = {11},
number = {1},
pages = {36:1--36:19},
year = {2019},
url = {https://doi.org/10.1186/s13321-019-0356-5},
doi = {10.1186/S13321-019-0356-5},
timestamp = {Wed, 01 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/AllenMMB19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/NguyenSLJVTWHVM19,
author = {Minh N. Nguyen and
Neeladri Sen and
Meiyin Lin and
Thomas Leonard Joseph and
Candida Vaz and
Vivek Tanavde and
Luke Way and
Ted R. Hupp and
Chandra S. Verma and
M. S. Madhusudhan},
title = {Discovering Putative Protein Targets of Small Molecules: {A} Study
of the p53 Activator Nutlin},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {4},
pages = {1529--1546},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.8b00762},
doi = {10.1021/ACS.JCIM.8B00762},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/NguyenSLJVTWHVM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/VitaLRTRB19,
author = {Simona De Vita and
Gianluigi Lauro and
Dafne Ruggiero and
Stefania Terracciano and
Raffaele Riccio and
Giuseppe Bifulco},
title = {Protein Preparation Automatic Protocol for High-Throughput Inverse
Virtual Screening: Accelerating the Target Identification by Computational
Methods},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {11},
pages = {4678--4690},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.9b00428},
doi = {10.1021/ACS.JCIM.9B00428},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/VitaLRTRB19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/WolfALVMGDBFSG19,
author = {Steffen Wolf and
Marta Amaral and
Maryse Lowinski and
Francois Vall{\'{e}}e and
Djordje Musil and
J{\"{o}}rn G{\"{u}}ldenhaupt and
Matthias K. Dreyer and
J{\"{o}}rg Bomke and
Matthias Frech and
J{\"{u}}rgen Schlitter and
Klaus Gerwert},
title = {Estimation of Protein-Ligand Unbinding Kinetics Using Non-Equilibrium
Targeted Molecular Dynamics Simulations},
journal = {J. Chem. Inf. Model.},
volume = {59},
number = {12},
pages = {5135--5147},
year = {2019},
url = {https://doi.org/10.1021/acs.jcim.9b00592},
doi = {10.1021/ACS.JCIM.9B00592},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/WolfALVMGDBFSG19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/DainaMZ19,
author = {Antoine Daina and
Olivier Michielin and
Vincent Zoete},
title = {SwissTargetPrediction: updated data and new features for efficient
prediction of protein targets of small molecules},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Webserver-Issue},
pages = {W357--W364},
year = {2019},
url = {https://doi.org/10.1093/nar/gkz382},
doi = {10.1093/NAR/GKZ382},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/DainaMZ19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ReyRTGM19,
author = {Julien Rey and
In{\`{e}}s Rasolohery and
Pierre Tuff{\'{e}}ry and
Fr{\'{e}}d{\'{e}}ric Guyon and
Gautier Moroy},
title = {PatchSearch: a web server for off-target protein identification},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Webserver-Issue},
pages = {W365--W372},
year = {2019},
url = {https://doi.org/10.1093/nar/gkz478},
doi = {10.1093/NAR/GKZ478},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ReyRTGM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/netmahib/AmalaE19,
author = {Arumugam Amala and
Isaac Arnold Emerson},
title = {Identification of target genes in cancer diseases using protein-protein
interaction networks},
journal = {Netw. Model. Anal. Health Informatics Bioinform.},
volume = {8},
number = {1},
pages = {2},
year = {2019},
url = {https://doi.org/10.1007/s13721-018-0181-1},
doi = {10.1007/S13721-018-0181-1},
timestamp = {Tue, 08 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/netmahib/AmalaE19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LeeKN19,
author = {Ingoo Lee and
Jongsoo Keum and
Hojung Nam},
title = {DeepConv-DTI: Prediction of drug-target interactions via deep learning
with convolution on protein sequences},
journal = {PLoS Comput. Biol.},
volume = {15},
number = {6},
year = {2019},
url = {https://doi.org/10.1371/journal.pcbi.1007129},
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timestamp = {Sat, 09 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/LeeKN19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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author = {Jianan Lin and
Yuping Zhang and
Wayne N. Frankel and
Zhengqing Ouyang},
title = {{PRAS:} Predicting functional targets of {RNA} binding proteins based
on CLIP-seq peaks},
journal = {PLoS Comput. Biol.},
volume = {15},
number = {8},
year = {2019},
url = {https://doi.org/10.1371/journal.pcbi.1007227},
doi = {10.1371/JOURNAL.PCBI.1007227},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/LinZFO19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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author = {V. K. Md. Aksam and
V. M. Chandrasekaran and
Pandurangan Sundaramurthy},
title = {Protein Domain Level Cancer Drug Targets in the Network of {MAPK}
Pathways},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {16},
number = {6},
pages = {2057--2065},
year = {2019},
url = {https://doi.org/10.1109/TCBB.2018.2829507},
doi = {10.1109/TCBB.2018.2829507},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/AksamCS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/MalhotraSJP19,
author = {Anvita Gupta Malhotra and
Sudha Singh and
Mohit Jha and
Khushhali Menaria Pandey},
title = {A Parametric Targetability Evaluation Approach for Vitiligo Proteome
Extracted through Integration of Gene Ontologies and Protein Interaction
Topologies},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {16},
number = {6},
pages = {1830--1842},
year = {2019},
url = {https://doi.org/10.1109/TCBB.2018.2835459},
doi = {10.1109/TCBB.2018.2835459},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/MalhotraSJP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/Caoili19,
author = {Salvador Eugenio C. Caoili},
editor = {Xinghua Mindy Shi and
Michael Buck and
Jian Ma and
Pierangelo Veltri},
title = {Toward a Sequence-Based Physicochemical Approach to Variable-Length
B-Cell Epitope Prediction for Antipeptide Paratopes Recognizing Flexibly
Disordered Targets: Insights Drawn from Protein Folding Modeled as
Polymer Collapse},
booktitle = {Proceedings of the 10th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, {BCB} 2019, Niagara
Falls, NY, USA, September 7-10, 2019},
pages = {534},
publisher = {{ACM}},
year = {2019},
url = {https://doi.org/10.1145/3307339.3343242},
doi = {10.1145/3307339.3343242},
timestamp = {Wed, 18 Sep 2019 17:06:08 +0200},
biburl = {https://dblp.org/rec/conf/bcb/Caoili19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@inproceedings{DBLP:conf/bibe/SaragihSAT19,
author = {Mutiara Saragih and
Filia Stephanie and
Ahmad Husein Alkaff and
Usman Sumo Friend Tambunan},
title = {Identification Novel Peptides Conjugated to {HIV1} Tat Peptide to
Inhibit Ebola Virus Entry by Targeting Niemann Pick {C1} Protein},
booktitle = {19th {IEEE} International Conference on Bioinformatics and Bioengineering,
{BIBE} 2019, Athens, Greece, October 28-30, 2019},
pages = {44--49},
publisher = {{IEEE}},
year = {2019},
url = {https://doi.org/10.1109/BIBE.2019.00017},
doi = {10.1109/BIBE.2019.00017},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bibe/SaragihSAT19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@inproceedings{DBLP:conf/iccabs/LiLL19,
author = {Jiefu Li and
Jung{-}Youn Lee and
Li Liao},
editor = {Ion I. Mandoiu and
T. M. Murali and
Giri Narasimhan and
Sanguthevar Rajasekaran and
Pavel Skums and
Alexander Zelikovsky},
title = {Detecting De Novo Plasmodesmata Targeting Signals and Identifying
{PD} Targeting Proteins},
booktitle = {Computational Advances in Bio and Medical Sciences - 9th International
Conference, {ICCABS} 2019, Miami, FL, USA, November 15-17, 2019, Revised
Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {12029},
pages = {1--12},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-46165-2\_1},
doi = {10.1007/978-3-030-46165-2\_1},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iccabs/LiLL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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author = {Andrei A. Ivanov and
Brian Revennaugh and
Lauren Rusnak and
Valentina Gonzalez{-}Pecchi and
Xiulei Mo and
Margaret A. Johns and
Yuhong Du and
Lee A. D. Cooper and
Carlos Sanchez Moreno and
Fadlo R. Khuri and
Haian Fu},
title = {The OncoPPi Portal: an integrative resource to explore and prioritize
protein-protein interactions for cancer target discovery},
journal = {Bioinform.},
volume = {34},
number = {7},
pages = {1183--1191},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/btx743},
doi = {10.1093/BIOINFORMATICS/BTX743},
timestamp = {Sun, 01 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/IvanovRRGMJDCMK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarzeBSG18,
author = {Nicholas A. Marze and
Shourya S. Roy Burman and
William Sheffler and
Jeffrey J. Gray},
title = {Efficient flexible backbone protein-protein docking for challenging
targets},
journal = {Bioinform.},
volume = {34},
number = {20},
pages = {3461--3469},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty355},
doi = {10.1093/BIOINFORMATICS/BTY355},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarzeBSG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@article{DBLP:journals/bmcsb/JungKBYL18,
author = {Jinmyung Jung and
Mijin Kwon and
Sunghwa Bae and
Soorin Yim and
Doheon Lee},
title = {Petri net-based prediction of therapeutic targets that recover abnormally
phosphorylated proteins in muscle atrophy},
journal = {{BMC} Syst. Biol.},
volume = {12},
number = {1},
pages = {26:1--26:11},
year = {2018},
url = {https://doi.org/10.1186/s12918-018-0555-0},
doi = {10.1186/S12918-018-0555-0},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/JungKBYL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/KhanAJLKCW18,
author = {Abbas Khan and
Arif Ali and
Muhammad Junaid and
Chang Liu and
Aman Chandra Kaushik and
William C. S. Cho and
Dong{-}Qing Wei},
title = {Identification of novel drug targets for diamond-blackfan anemia based
on {RPS19} gene mutation using protein-protein interaction network},
journal = {{BMC} Syst. Biol.},
volume = {12},
number = {4},
pages = {5--16},
year = {2018},
url = {https://doi.org/10.1186/s12918-018-0563-0},
doi = {10.1186/S12918-018-0563-0},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/KhanAJLKCW18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/ChiraniGGPSDH18,
author = {Alireza Salimi Chirani and
Mona Ghazi and
Mehdi Goudarzi and
Shahin Najar Peerayeh and
Hoorieh Soleimanjahi and
Masoud Dadashi and
Bahareh Hajikhani},
title = {A survey on chimeric UreB\({}_{\mbox{229-561}}\)-HpaA protein targeting
\emph{Helicobacter pylori}: Computational and \emph{in vitro} urease
activity valuation},
journal = {Comput. Biol. Chem.},
volume = {76},
pages = {42--52},
year = {2018},
url = {https://doi.org/10.1016/j.compbiolchem.2018.05.001},
doi = {10.1016/J.COMPBIOLCHEM.2018.05.001},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/ChiraniGGPSDH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/ChiraniMPHNGGO18,
author = {Alireza Salimi Chirani and
Robabeh Majidzadeh and
Ramin Pouriran and
Mohsen Heidary and
Mohammad Javad Nasiri and
Mehrdad Gholami and
Mehdi Goudarzi and
Vahid Fallah Omrani},
title = {The effect of in silico targeting \emph{Pseudomonas aeruginosa} patatin-like
protein D, for immunogenic administration},
journal = {Comput. Biol. Chem.},
volume = {74},
pages = {12--19},
year = {2018},
url = {https://doi.org/10.1016/j.compbiolchem.2018.02.001},
doi = {10.1016/J.COMPBIOLCHEM.2018.02.001},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/ChiraniMPHNGGO18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/Palanisamy18,
author = {Navaneethan Palanisamy},
title = {Identification of putative drug targets and annotation of unknown
proteins in \emph{Tropheryma whipplei}},
journal = {Comput. Biol. Chem.},
volume = {76},
pages = {130--138},
year = {2018},
url = {https://doi.org/10.1016/j.compbiolchem.2018.05.024},
doi = {10.1016/J.COMPBIOLCHEM.2018.05.024},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/Palanisamy18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/PriyaKH18,
author = {S. Priya and
Nachimuthu Senthil Kumar and
S. Hemalatha},
title = {Antiviral phytocompounds target envelop protein to control Zika virus},
journal = {Comput. Biol. Chem.},
volume = {77},
pages = {402--412},
year = {2018},
url = {https://doi.org/10.1016/j.compbiolchem.2018.08.008},
doi = {10.1016/J.COMPBIOLCHEM.2018.08.008},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/candc/PriyaKH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/UddinJ18,
author = {Reaz Uddin and
Faiza Jamil},
title = {Prioritization of potential drug targets against \emph{P. aeruginosa}
by core proteomic analysis using computational subtractive genomics
and Protein-Protein interaction network},
journal = {Comput. Biol. Chem.},
volume = {74},
pages = {115--122},
year = {2018},
url = {https://doi.org/10.1016/j.compbiolchem.2018.02.017},
doi = {10.1016/J.COMPBIOLCHEM.2018.02.017},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/UddinJ18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/McGarryM18,
author = {Ken McGarry and
Sharon McDonald},
title = {Complex network theory for the identification and assessment of candidate
protein targets},
journal = {Comput. Biol. Medicine},
volume = {97},
pages = {113--123},
year = {2018},
url = {https://doi.org/10.1016/j.compbiomed.2018.04.015},
doi = {10.1016/J.COMPBIOMED.2018.04.015},
timestamp = {Wed, 02 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/McGarryM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijbra/PrabaharSRVJN18,
author = {Archana Prabahar and
Subashini Swaminathan and
Kalpana Raja and
Srividhya Vellingiri and
Ramalingam Jegadeesan and
Bharathi Nathan},
title = {Discovery of novel inhibitors targeting movement protein for controlling
the transmission of banana bunchy top virus infection in plantain
by structure-based virtual screening},
journal = {Int. J. Bioinform. Res. Appl.},
volume = {14},
number = {4},
pages = {305--320},
year = {2018},
url = {https://doi.org/10.1504/IJBRA.2018.10009939},
doi = {10.1504/IJBRA.2018.10009939},
timestamp = {Fri, 11 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijbra/PrabaharSRVJN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijcbdd/KordbachehNF18,
author = {Emad Kordbacheh and
Shahram Nazarian and
Amin Farhang},
title = {An in silico approach for construction of a chimeric protein, targeting
virulence factors of Shigella spp},
journal = {Int. J. Comput. Biol. Drug Des.},
volume = {11},
number = {4},
pages = {310--327},
year = {2018},
url = {https://doi.org/10.1504/IJCBDD.2018.096127},
doi = {10.1504/IJCBDD.2018.096127},
timestamp = {Sat, 25 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijcbdd/KordbachehNF18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/RabalCO18,
author = {Obdulia Rabal and
Andrea Castellar and
Julen Oyarzabal},
title = {Novel pharmacological maps of protein lysine methyltransferases: key
for target deorphanization},
journal = {J. Cheminformatics},
volume = {10},
number = {1},
pages = {32:1--32:19},
year = {2018},
url = {https://doi.org/10.1186/s13321-018-0288-5},
doi = {10.1186/S13321-018-0288-5},
timestamp = {Wed, 25 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/RabalCO18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/ZhouCS18,
author = {Hongyi Zhou and
Hongnan Cao and
Jeffrey Skolnick},
title = {FINDSITEcomb2.0: {A} New Approach for Virtual Ligand Screening of
Proteins and Virtual Target Screening of Biomolecules},
journal = {J. Chem. Inf. Model.},
volume = {58},
number = {11},
pages = {2343--2354},
year = {2018},
url = {https://doi.org/10.1021/acs.jcim.8b00309},
doi = {10.1021/ACS.JCIM.8B00309},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/ZhouCS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/PabonXEYHSBAGBC18,
author = {Nicolas A. Pabon and
Yan Xia and
Samuel K. Estabrooks and
Zhaofeng Ye and
Amanda K. Herbrand and
Evelyn S{\"{u}}{\ss} and
Ricardo M. Biondi and
Victoria A. Assimon and
Jason E. Gestwicki and
Jeffrey L. Brodsky and
Carlos J. Camacho and
Ziv Bar{-}Joseph},
title = {Predicting protein targets for drug-like compounds using transcriptomics},
journal = {PLoS Comput. Biol.},
volume = {14},
number = {12},
year = {2018},
url = {https://doi.org/10.1371/journal.pcbi.1006651},
doi = {10.1371/JOURNAL.PCBI.1006651},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/PabonXEYHSBAGBC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/WesterlundD18,
author = {Annie M. Westerlund and
Lucie Delemotte},
title = {Effect of Ca2+ on the promiscuous target-protein binding of calmodulin},
journal = {PLoS Comput. Biol.},
volume = {14},
number = {4},
year = {2018},
url = {https://doi.org/10.1371/journal.pcbi.1006072},
doi = {10.1371/JOURNAL.PCBI.1006072},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/WesterlundD18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/ChenCCT18,
author = {Jhih{-}Ying Chen and
Chia{-}Min Chen and
Pei{-}Chun Chang and
Jeffrey J. P. Tsai},
title = {The Potential Dual-Target Inhibitors for {HER2/HSP90} Proteins from
Traditional Chinese Medicine},
booktitle = {18th {IEEE} International Conference on Bioinformatics and Bioengineering,
{BIBE} 2018, Taichung, Taiwan, October 29-31, 2018},
pages = {277--282},
publisher = {{IEEE}},
year = {2018},
url = {https://doi.org/10.1109/BIBE.2018.00061},
doi = {10.1109/BIBE.2018.00061},
timestamp = {Wed, 16 Oct 2019 14:14:56 +0200},
biburl = {https://dblp.org/rec/conf/bibe/ChenCCT18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/KumarZSLS18,
author = {Sajal Kumar and
Hua Zhong and
Ruby Sharma and
Yiyi Li and
Mingzhou Song},
editor = {Huiru Jane Zheng and
Zoraida Callejas and
David Griol and
Haiying Wang and
Xiaohua Hu and
Harald H. H. W. Schmidt and
Jan Baumbach and
Julie Dickerson and
Le Zhang},
title = {Scrutinizing functional interaction networks from RNA-binding proteins
to their targets in cancer},
booktitle = {{IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2018, Madrid, Spain, December 3-6, 2018},
pages = {185--190},
publisher = {{IEEE} Computer Society},
year = {2018},
url = {https://doi.ieeecomputersociety.org/10.1109/BIBM.2018.8621502},
doi = {10.1109/BIBM.2018.8621502},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/KumarZSLS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/MaAZH18,
author = {Jun Ma and
Hongxin An and
Ruisheng Zhang and
Rongjing Hu},
editor = {Huiru Jane Zheng and
Zoraida Callejas and
David Griol and
Haiying Wang and
Xiaohua Hu and
Harald H. H. W. Schmidt and
Jan Baumbach and
Julie Dickerson and
Le Zhang},
title = {Collaborative Filtering based Recommendation Algorithm for Recommending
Active Molecules for Protein Targets},
booktitle = {{IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2018, Madrid, Spain, December 3-6, 2018},
pages = {1203--1208},
publisher = {{IEEE} Computer Society},
year = {2018},
url = {https://doi.ieeecomputersociety.org/10.1109/BIBM.2018.8621560},
doi = {10.1109/BIBM.2018.8621560},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/MaAZH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cicba/BasakBSCBN18,
author = {Soukhindra Nath Basak and
Ankur Kumar Biswas and
Sovan Saha and
Piyali Chatterjee and
Subhadip Basu and
Mita Nasipuri},
editor = {Jyotsna Kumar Mandal and
Somnath Mukhopadhyay and
Paramartha Dutta and
Kousik Dasgupta},
title = {Target Protein Function Prediction by Identification of Essential
Proteins in Protein-Protein Interaction Network},
booktitle = {Computational Intelligence, Communications, and Business Analytics
- Second International Conference, {CICBA} 2018, Kalyani, India, July
27-28, 2018, Revised Selected Papers, Part {II}},
series = {Communications in Computer and Information Science},
volume = {1031},
pages = {219--231},
publisher = {Springer},
year = {2018},
url = {https://doi.org/10.1007/978-981-13-8581-0\_18},
doi = {10.1007/978-981-13-8581-0\_18},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cicba/BasakBSCBN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icic/LeeLH18,
author = {Wook Lee and
Jisu Lee and
Kyungsook Han},
editor = {De{-}Shuang Huang and
Vitoantonio Bevilacqua and
Prashan Premaratne and
Phalguni Gupta},
title = {Finding Potential {RNA} Aptamers for a Protein Target Using Sequence
and Structure Features},
booktitle = {Intelligent Computing Theories and Application - 14th International
Conference, {ICIC} 2018, Wuhan, China, August 15-18, 2018, Proceedings,
Part {I}},
series = {Lecture Notes in Computer Science},
volume = {10954},
pages = {888--892},
publisher = {Springer},
year = {2018},
url = {https://doi.org/10.1007/978-3-319-95930-6\_89},
doi = {10.1007/978-3-319-95930-6\_89},
timestamp = {Tue, 14 May 2019 10:00:53 +0200},
biburl = {https://dblp.org/rec/conf/icic/LeeLH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1811-02114,
author = {Ingoo Lee and
Jongsoo Keum and
Hojung Nam},
title = {DeepConv-DTI: Prediction of drug-target interactions via deep learning
with convolution on protein sequences},
journal = {CoRR},
volume = {abs/1811.02114},
year = {2018},
url = {http://arxiv.org/abs/1811.02114},
eprinttype = {arXiv},
eprint = {1811.02114},
timestamp = {Mon, 26 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1811-02114.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangTZQCZLJCC17,
author = {Peng Zhang and
Lin Tao and
Xian Zeng and
Chu Qin and
Shangying Chen and
Feng Zhu and
Zerong Li and
Yu Yang Jiang and
Weiping Chen and
Yuzong Chen},
title = {A protein network descriptor server and its use in studying protein,
disease, metabolic and drug targeted networks},
journal = {Briefings Bioinform.},
volume = {18},
number = {6},
pages = {1057--1070},
year = {2017},
url = {https://doi.org/10.1093/bib/bbw071},
doi = {10.1093/BIB/BBW071},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangTZQCZLJCC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BienvenutSDMG17,
author = {Willy Vincent Bienvenut and
Jean{-}Pierre Scarpelli and
Johan Dumestier and
Thierry Meinnel and
Carmela Giglione},
title = {EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted
proteins in complex samples},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {182:1--182:13},
year = {2017},
url = {https://doi.org/10.1186/s12859-017-1595-y},
doi = {10.1186/S12859-017-1595-Y},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BienvenutSDMG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KimJHPL17,
author = {Baeksoo Kim and
Jihoon Jo and
Jonghyun Han and
Chungoo Park and
Hyunju Lee},
title = {In silico re-identification of properties of drug target proteins},
journal = {{BMC} Bioinform.},
volume = {18},
number = {7},
pages = {35--44},
year = {2017},
url = {https://doi.org/10.1186/s12859-017-1639-3},
doi = {10.1186/S12859-017-1639-3},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KimJHPL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/AppunniRRCSS17,
author = {Sandeep Appunni and
P. M. Rajisha and
Muni Rubens and
Sangoju Chandana and
Himanshu Narayan Singh and
Vishnu Swarup},
title = {Targeting PknB, an eukaryotic-like serine/threonine protein kinase
of Mycobacterium tuberculosis with phytomolecules},
journal = {Comput. Biol. Chem.},
volume = {67},
pages = {200--204},
year = {2017},
url = {https://doi.org/10.1016/j.compbiolchem.2017.01.003},
doi = {10.1016/J.COMPBIOLCHEM.2017.01.003},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/candc/AppunniRRCSS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/GahoiG17,
author = {Shachi Gahoi and
Budhayash Gautam},
title = {Genome-wide analysis of Excretory/Secretory proteins in root-knot
nematode, Meloidogyne incognita provides potential targets for parasite
control},
journal = {Comput. Biol. Chem.},
volume = {67},
pages = {225--233},
year = {2017},
url = {https://doi.org/10.1016/j.compbiolchem.2017.01.014},
doi = {10.1016/J.COMPBIOLCHEM.2017.01.014},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/candc/GahoiG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/ReddyRY17,
author = {G. Koteswara Reddy and
K. Nagamalleswara Rao and
Kiran Yarrakula},
title = {Insights into structure and function of 30S Ribosomal Protein {S2}
{(30S2)} in Chlamydophila pneumoniae: {A} potent target of pneumonia},
journal = {Comput. Biol. Chem.},
volume = {66},
pages = {11--20},
year = {2017},
url = {https://doi.org/10.1016/j.compbiolchem.2016.10.014},
doi = {10.1016/J.COMPBIOLCHEM.2016.10.014},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/candc/ReddyRY17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/ThayerH17,
author = {Kelly M. Thayer and
In Sub M. Han},
title = {Chemical principles additive model aligns low consensus {DNA} targets
of p53 tumor suppressor protein},
journal = {Comput. Biol. Chem.},
volume = {68},
pages = {186--193},
year = {2017},
url = {https://doi.org/10.1016/j.compbiolchem.2017.03.003},
doi = {10.1016/J.COMPBIOLCHEM.2017.03.003},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/candc/ThayerH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/XuBCBJZZT17,
author = {Darong Xu and
Hongliang Bian and
Jinlan Cai and
Daocheng Bao and
Qing Jin and
Min Zhu and
Cuifeng Zhang and
Tingting Tao},
title = {Computational design of peptide ligands to target the intermolecular
interaction between viral envelope protein and pediatric receptor},
journal = {Comput. Biol. Chem.},
volume = {69},
pages = {120--125},
year = {2017},
url = {https://doi.org/10.1016/j.compbiolchem.2017.06.001},
doi = {10.1016/J.COMPBIOLCHEM.2017.06.001},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/candc/XuBCBJZZT17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijcbdd/KumariC17,
author = {Madhulata Kumari and
Subhash Chandra},
title = {In silico prediction and evaluation of interaction between protein
arginine N-methyltransferase 5 cancer target and curcumin derivatives
by molecular docking and simulation},
journal = {Int. J. Comput. Biol. Drug Des.},
volume = {10},
number = {1},
pages = {79--86},
year = {2017},
url = {https://doi.org/10.1504/IJCBDD.2017.10003751},
doi = {10.1504/IJCBDD.2017.10003751},
timestamp = {Sat, 25 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijcbdd/KumariC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijcbdd/SitoteG17,
author = {Tilahun Melak Sitote and
Sunita Gakkhar},
title = {Structural analysis of protein translocase subunit SecY from Mycobacterium
tuberculosis H37Rv: a potential target for anti-tuberculosis drug
discovery},
journal = {Int. J. Comput. Biol. Drug Des.},
volume = {10},
number = {4},
pages = {374--386},
year = {2017},
url = {https://doi.org/10.1504/IJCBDD.2017.10009087},
doi = {10.1504/IJCBDD.2017.10009087},
timestamp = {Sat, 25 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijcbdd/SitoteG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijcbdd/SriramanSR17,
author = {Shraddha Sriraman and
Nanda Gopal Saha and
Sujata Roy},
title = {Interaction of curcumin with different target proteins of Alzheimer's
disease: docking and {MD} simulation studies},
journal = {Int. J. Comput. Biol. Drug Des.},
volume = {10},
number = {4},
pages = {315--330},
year = {2017},
url = {https://doi.org/10.1504/IJCBDD.2017.10009070},
doi = {10.1504/IJCBDD.2017.10009070},
timestamp = {Sat, 25 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijcbdd/SriramanSR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/KalashVALSZMLBG17,
author = {Leen Kalash and
Cristina Val and
Jhonny Azuaje and
Maria Isabel Loza and
Fredrik Svensson and
Azedine Zoufir and
Lewis H. Mervin and
Graham Ladds and
Jos{\'{e}} M. Brea and
Robert C. Glen and
Eddy Sotelo and
Andreas Bender},
title = {Computer-aided design of multi-target ligands at A1R, {A2AR} and PDE10A,
key proteins in neurodegenerative diseases},
journal = {J. Cheminformatics},
volume = {9},
number = {1},
pages = {67:1--67:19},
year = {2017},
url = {https://doi.org/10.1186/s13321-017-0249-4},
doi = {10.1186/S13321-017-0249-4},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/KalashVALSZMLBG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BaiHZLZ17,
author = {Zhengya Bai and
Shasha Hou and
Shilei Zhang and
Zhongyan Li and
Peng Zhou},
title = {Targeting Self-Binding Peptides as a Novel Strategy To Regulate Protein
Activity and Function: {A} Case Study on the Proto-oncogene Tyrosine
Protein Kinase \emph{c}-Src},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {4},
pages = {835--845},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.6b00673},
doi = {10.1021/ACS.JCIM.6B00673},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/BaiHZLZ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LiYLHYLY17,
author = {Guo{-}Bo Li and
Zhu{-}Jun Yu and
Sha Liu and
Lu{-}Yi Huang and
Ling{-}Ling Yang and
Christopher T. Lohans and
Sheng{-}Yong Yang},
title = {IFPTarget: {A} Customized Virtual Target Identification Method Based
on Protein-Ligand Interaction Fingerprinting Analyses},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {7},
pages = {1640--1651},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.7b00225},
doi = {10.1021/ACS.JCIM.7B00225},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/LiYLHYLY17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/WangWX17,
author = {Nanyi Wang and
Lirong Wang and
Xiang{-}Qun Xie},
title = {ProSelection: {A} Novel Algorithm to Select Proper Protein Structure
Subsets for in Silico Target Identification and Drug Discovery Research},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {11},
pages = {2686--2698},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.7b00277},
doi = {10.1021/ACS.JCIM.7B00277},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/WangWX17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/XingLLWXZSJLCJLZ17,
author = {Jing Xing and
Wenchao Lu and
Rongfeng Liu and
Yulan Wang and
Yiqian Xie and
Hao Zhang and
Zhe Shi and
Hao Jiang and
Yu{-}Chih Liu and
Kaixian Chen and
Hualiang Jiang and
Cheng Luo and
Mingyue Zheng},
title = {Machine-Learning-Assisted Approach for Discovering Novel Inhibitors
Targeting Bromodomain-Containing Protein 4},
journal = {J. Chem. Inf. Model.},
volume = {57},
number = {7},
pages = {1677--1690},
year = {2017},
url = {https://doi.org/10.1021/acs.jcim.7b00098},
doi = {10.1021/ACS.JCIM.7B00098},
timestamp = {Fri, 08 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/XingLLWXZSJLCJLZ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/VargaDRT17,
author = {Julia Varga and
L{\'{a}}szl{\'{o}} Dobson and
Istv{\'{a}}n Rem{\'{e}}nyi and
G{\'{a}}bor E. Tusn{\'{a}}dy},
title = {{TSTMP:} target selection for structural genomics of human transmembrane
proteins},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Database-Issue},
pages = {D325--D330},
year = {2017},
url = {https://doi.org/10.1093/nar/gkw939},
doi = {10.1093/NAR/GKW939},
timestamp = {Tue, 06 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/VargaDRT17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nature/ChevalierSRHVMB17,
author = {Aaron Chevalier and
Daniel{-}Adriano Silva and
Gabriel J. Rocklin and
Derrick R. Hicks and
Renan Vergara and
Patience Murapa and
Steffen M. Bernard and
Lu Zhang and
Kwok{-}Ho Lam and
Guorui Yao and
Christopher D. Bahl and
Shin{-}Ichiro Miyashita and
Inna Goreshnik and
James T. Fuller and
Merika T. Koday and
Cody M. Jenkins and
Tom Colvin and
Lauren P. Carter and
Alan Bohn and
Cassie M. Bryan and
D. Alejandro Fern{\'{a}}ndez{-}Velasco and
Lance J. Stewart and
Min Dong and
Xuhui Huang and
Rongsheng Jin and
Ian A. Wilson and
Deborah H. Fuller and
David Baker},
title = {Massively parallel \emph{de novo} protein design for targeted therapeutics},
journal = {Nat.},
volume = {550},
number = {7674},
pages = {74--79},
year = {2017},
url = {https://doi.org/10.1038/nature23912},
doi = {10.1038/NATURE23912},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nature/ChevalierSRHVMB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/sensors/ImamuraMSYFN17,
author = {Ryota Imamura and
Naoki Murata and
Toshinori Shimanouchi and
Kaoru Yamashita and
Masayuki Fukuzawa and
Minoru Noda},
title = {A Label-Free Fluorescent Array Sensor Utilizing Liposome Encapsulating
Calcein for Discriminating Target Proteins by Principal Component
Analysis},
journal = {Sensors},
volume = {17},
number = {7},
pages = {1630},
year = {2017},
url = {https://doi.org/10.3390/s17071630},
doi = {10.3390/S17071630},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/sensors/ImamuraMSYFN17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/SinhaSPPDK17,
author = {Arvind Kumar Sinha and
Pradeep Singh and
Anand Prakash and
Dharm Pal and
Anuradha Dube and
Awanish Kumar},
title = {Putative Drug and Vaccine Target Identification in Leishmania donovani
Membrane Proteins Using Na{\"{\i}}ve Bayes Probabilistic Classifier},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {14},
number = {1},
pages = {204--211},
year = {2017},
url = {https://doi.org/10.1109/TCBB.2016.2570217},
doi = {10.1109/TCBB.2016.2570217},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/SinhaSPPDK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/ZhengYLG17,
author = {Guang Zheng and
Yun Yang and
Chengqiang Li and
Hongtao Guo},
editor = {Xiaohua Hu and
Chi{-}Ren Shyu and
Yana Bromberg and
Jean Gao and
Yang Gong and
Dmitry Korkin and
Illhoi Yoo and
Huiru Jane Zheng},
title = {Functional protein-protein interaction networks regulated by 6-gingerol
targeting stomach and small intestine},
booktitle = {2017 {IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2017, Kansas City, MO, USA, November 13-16, 2017},
pages = {1413--1419},
publisher = {{IEEE} Computer Society},
year = {2017},
url = {https://doi.org/10.1109/BIBM.2017.8217870},
doi = {10.1109/BIBM.2017.8217870},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/ZhengYLG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csbio/SiamHKR17,
author = {Mohammad Kawsar Sharif Siam and
Muhammad Sameer Hossain and
Eva Rahman Kabir and
Samiul Alam Rajib},
title = {In Silico Structure Based Designing of Dihydrofolate Reductase Enzyme
Antagonists and Potential Small Molecules That Target {DHFR} Protein
to Inhibit the Folic Acid Biosynthetic Pathways},
booktitle = {Proceedings of the 8th International Conference on Computational Systems-Biology
and Bioinformatics, Nha Trang City, Viet Nam, December 7-8, 2017},
pages = {62--67},
publisher = {{ACM}},
year = {2017},
url = {https://doi.org/10.1145/3156346.3156358},
doi = {10.1145/3156346.3156358},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/csbio/SiamHKR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/WangYCXLYZ17,
author = {Lei Wang and
Zhu{-}Hong You and
Xing Chen and
Shixiong Xia and
Feng Liu and
Xin Yan and
Yong Zhou},
editor = {Zhipeng Cai and
Ovidiu Daescu and
Min Li},
title = {Computational Methods for the Prediction of Drug-Target Interactions
from Drug Fingerprints and Protein Sequences by Stacked Auto-Encoder
Deep Neural Network},
booktitle = {Bioinformatics Research and Applications - 13th International Symposium,
{ISBRA} 2017, Honolulu, HI, USA, May 29 - June 2, 2017, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10330},
pages = {46--58},
publisher = {Springer},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-59575-7\_5},
doi = {10.1007/978-3-319-59575-7\_5},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/WangYCXLYZ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stringology/RistovVS17,
author = {Strahil Ristov and
Robert Vaser and
Mile Sikic},
editor = {Jan Holub and
Jan Zd{\'{a}}rek},
title = {Trade-offs in Query and Target Indexing for the Selection of Candidates
in Protein Homology Searches},
booktitle = {Proceedings of the Prague Stringology Conference 2017, Prague, Czech
Republic, August 28-30, 2017},
pages = {118--125},
publisher = {Department of Theoretical Computer Science, Faculty of Information
Technology, Czech Technical University in Prague},
year = {2017},
url = {http://www.stringology.org/event/2017/p12.html},
timestamp = {Wed, 10 Feb 2021 08:42:21 +0100},
biburl = {https://dblp.org/rec/conf/stringology/RistovVS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/KunzLNCD16,
author = {Meik Kunz and
Chunguang Liang and
Santosh Nilla and
Alexander Cecil and
Thomas Dandekar},
title = {The drug-minded protein interaction database (DrumPID) for efficient
target analysis and drug development},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016},
url = {https://doi.org/10.1093/database/baw041},
doi = {10.1093/DATABASE/BAW041},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/KunzLNCD16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangCDW16,
author = {Yong{-}Cui Wang and
Shi{-}Long Chen and
Nai{-}Yang Deng and
Yong Wang},
title = {Computational probing protein-protein interactions targeting small
molecules},
journal = {Bioinform.},
volume = {32},
number = {2},
pages = {226--234},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv528},
doi = {10.1093/BIOINFORMATICS/BTV528},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangCDW16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/Mutowo-Meullenet16,
author = {Prudence Mutowo{-}Meullenet and
A. Patr{\'{\i}}cia Bento and
Nathan Dedman and
Anna Gaulton and
Anne Hersey and
Jane Lomax and
John P. Overington},
title = {A drug target slim: using gene ontology and gene ontology annotations
to navigate protein-ligand target space in ChEMBL},
journal = {J. Biomed. Semant.},
volume = {7},
pages = {59},
year = {2016},
url = {https://doi.org/10.1186/s13326-016-0102-0},
doi = {10.1186/S13326-016-0102-0},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/Mutowo-Meullenet16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KeumYLN16,
author = {Jongsoo Keum and
Sunyong Yoo and
Doheon Lee and
Hojung Nam},
title = {Prediction of compound-target interactions of natural products using
large-scale drug and protein information},
journal = {{BMC} Bioinform.},
volume = {17},
number = {{S-6}},
pages = {219},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-1081-y},
doi = {10.1186/S12859-016-1081-Y},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KeumYLN16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijcbdd/KhanJARAIAH16,
author = {Shama Khan and
Mohammad Sarwar Jamal and
Farah Anjum and
Mahmood Rasool and
Abulaish Ansari and
Asimul Islam and
Faizan Ahmad and
Md. Imtaiyaz Hassan},
title = {Functional annotation of putative conserved proteins from Borrelia
burgdorferi to find potential drug targets},
journal = {Int. J. Comput. Biol. Drug Des.},
volume = {9},
number = {4},
pages = {295--318},
year = {2016},
url = {https://doi.org/10.1504/IJCBDD.2016.10000929},
doi = {10.1504/IJCBDD.2016.10000929},
timestamp = {Sat, 25 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijcbdd/KhanJARAIAH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/DuS16,
author = {Yu Du and
Tieliu Shi},
title = {Ligand cluster-based protein network and ePlatton, a multi-target
ligand finder},
journal = {J. Cheminformatics},
volume = {8},
number = {1},
pages = {23:1--23:12},
year = {2016},
url = {https://doi.org/10.1186/s13321-016-0135-5},
doi = {10.1186/S13321-016-0135-5},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/DuS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/VilarH16,
author = {Santiago Vilar and
George Hripcsak},
title = {Leveraging 3D chemical similarity, target and phenotypic data in the
identification of drug-protein and drug-adverse effect associations},
journal = {J. Cheminformatics},
volume = {8},
number = {1},
pages = {35:1--35:12},
year = {2016},
url = {https://doi.org/10.1186/s13321-016-0147-1},
doi = {10.1186/S13321-016-0147-1},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/VilarH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/GuoTCX16,
author = {Zuojun Guo and
Atli Thorarensen and
Jianwei Che and
Li Xing},
title = {Target the More Druggable Protein States in a Highly Dynamic Protein-Protein
Interaction System},
journal = {J. Chem. Inf. Model.},
volume = {56},
number = {1},
pages = {35--45},
year = {2016},
url = {https://doi.org/10.1021/acs.jcim.5b00503},
doi = {10.1021/ACS.JCIM.5B00503},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/GuoTCX16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SouthanSBFPABDM16,
author = {Christopher Southan and
Joanna L. Sharman and
Helen E. Benson and
Elena Faccenda and
Adam J. Pawson and
Stephen P. H. Alexander and
Oscar Peter Buneman and
Anthony P. Davenport and
John C. McGrath and
John A. Peters and
Michael Spedding and
William A. Catterall and
Doriano Fabbro and
Jamie A. Davies and
NC{-}IUPHAR},
title = {The {IUPHAR/BPS} Guide to {PHARMACOLOGY} in 2016: towards curated
quantitative interactions between 1300 protein targets and 6000 ligands},
journal = {Nucleic Acids Res.},
volume = {44},
number = {Database-Issue},
pages = {1054--1068},
year = {2016},
url = {https://doi.org/10.1093/nar/gkv1037},
doi = {10.1093/NAR/GKV1037},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/SouthanSBFPABDM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/Verkhivker16,
author = {Gennady M. Verkhivker},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein and
Marylyn D. Ritchie},
title = {Integrating Genetic and Structural Data on Human Protein Kinome in
Network-Based Modeling of Kinase Sensitivities and Resistance to Targeted
and Personalized Anticancer Drugs},
booktitle = {Biocomputing 2016: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 4-8, 2016},
pages = {45--56},
year = {2016},
url = {http://psb.stanford.edu/psb-online/proceedings/psb16/verkhivker.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/Verkhivker16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/abi/OferkinKSKSVS15,
author = {Igor Oferkin and
Ekaterina V. Katkova and
Alexey V. Sulimov and
Danil C. Kutov and
Sergey I. Sobolev and
Vladimir V. Voevodin and
Vladimir B. Sulimov},
title = {Evaluation of Docking Target Functions by the Comprehensive Investigation
of Protein-Ligand Energy Minima},
journal = {Adv. Bioinformatics},
volume = {2015},
pages = {126858:1--126858:12},
year = {2015},
url = {https://doi.org/10.1155/2015/126858},
doi = {10.1155/2015/126858},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/abi/OferkinKSKSVS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GfellerZ15,
author = {David Gfeller and
Vincent Zoete},
title = {Protein homology reveals new targets for bioactive small molecules},
journal = {Bioinform.},
volume = {31},
number = {16},
pages = {2721--2727},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv214},
doi = {10.1093/BIOINFORMATICS/BTV214},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GfellerZ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SavojardoMFC15,
author = {Castrense Savojardo and
Pier Luigi Martelli and
Piero Fariselli and
Rita Casadio},
title = {TPpred3 detects and discriminates mitochondrial and chloroplastic
targeting peptides in eukaryotic proteins},
journal = {Bioinform.},
volume = {31},
number = {20},
pages = {3269--3275},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv367},
doi = {10.1093/BIOINFORMATICS/BTV367},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SavojardoMFC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SunZZX15,
author = {Jingchun Sun and
Kevin W. Zhu and
W. Jim Zheng and
Hua Xu},
title = {A comparative study of disease genes and drug targets in the human
protein interactome},
journal = {{BMC} Bioinform.},
volume = {16},
number = {{S-5}},
pages = {S1},
year = {2015},
url = {https://doi.org/10.1186/1471-2105-16-S5-S1},
doi = {10.1186/1471-2105-16-S5-S1},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SunZZX15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/MarinGMKSJSCS15,
author = {Traci L. Marin and
Brendan Gongol and
Marcy Martin and
Stephanie J. King and
Lemar Smith and
David A. Johnson and
Shankar Subramaniam and
Shu Chien and
John Shyy},
title = {Identification of AMP-activated protein kinase targets by a consensus
sequence search of the proteome},
journal = {{BMC} Syst. Biol.},
volume = {9},
pages = {13},
year = {2015},
url = {https://doi.org/10.1186/s12918-015-0156-0},
doi = {10.1186/S12918-015-0156-0},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/MarinGMKSJSCS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/SabetianS15,
author = {Soudabeh Sabetian and
Mohd Shahir Shamsir},
title = {Identification of putative drug targets for human sperm-egg interaction
defect using protein network approach},
journal = {{BMC} Syst. Biol.},
volume = {9},
pages = {37},
year = {2015},
url = {https://doi.org/10.1186/s12918-015-0186-7},
doi = {10.1186/S12918-015-0186-7},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/SabetianS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/WangLLDH15,
author = {Caihua Wang and
Juan Liu and
Fei Luo and
Zixing Deng and
Qian{-}Nan Hu},
title = {Predicting target-ligand interactions using protein ligand-binding
site and ligand substructures},
journal = {{BMC} Syst. Biol.},
volume = {9},
number = {{S-1}},
pages = {S2},
year = {2015},
url = {https://doi.org/10.1186/1752-0509-9-S1-S2},
doi = {10.1186/1752-0509-9-S1-S2},
timestamp = {Tue, 21 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/WangLLDH15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/FuGWLPLZ15,
author = {Yuanyuan Fu and
Yanzhi Guo and
Yuelong Wang and
Jiesi Luo and
Xuemei Pu and
Menglong Li and
Zhihang Zhang},
title = {Exploring the relationship between hub proteins and drug targets based
on {GO} and intrinsic disorder},
journal = {Comput. Biol. Chem.},
volume = {56},
pages = {41--48},
year = {2015},
url = {https://doi.org/10.1016/j.compbiolchem.2015.03.003},
doi = {10.1016/J.COMPBIOLCHEM.2015.03.003},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/candc/FuGWLPLZ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/HalimJIMMH15,
author = {Sobia Ahsan Halim and
Muhammad Jawad and
Muhammad Ilyas and
Zulfiqar Mir and
Atif Anwar Mirza and
Tayyab Husnain},
title = {In silico identification of novel IL-1{\(\beta\)} inhibitors to target
protein-protein interfaces},
journal = {Comput. Biol. Chem.},
volume = {58},
pages = {158--166},
year = {2015},
url = {https://doi.org/10.1016/j.compbiolchem.2015.06.004},
doi = {10.1016/J.COMPBIOLCHEM.2015.06.004},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/candc/HalimJIMMH15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/comvis/KnodelNRRVTHW15,
author = {Markus M. Knodel and
Arne N{\"{a}}gel and
Sebastian Reiter and
Martin Rupp and
Andreas Vogel and
Paul Targett{-}Adams and
Eva Herrmann and
Gabriel Wittum},
title = {Multigrid analysis of spatially resolved hepatitis {C} virus protein
simulations},
journal = {Comput. Vis. Sci.},
volume = {17},
number = {5},
pages = {235--253},
year = {2015},
url = {https://doi.org/10.1007/s00791-016-0261-7},
doi = {10.1007/S00791-016-0261-7},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/comvis/KnodelNRRVTHW15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijbra/VaidyaP15,
author = {Megha Vaidya and
Hetalkumar Panchal},
title = {To study percentage distribution of target genes encoding proteins
of different classes in Helicobacter pylori strain {J99} and identification
of potential therapeutic targets to reduce its proliferation},
journal = {Int. J. Bioinform. Res. Appl.},
volume = {11},
number = {1},
pages = {1--9},
year = {2015},
url = {https://doi.org/10.1504/IJBRA.2015.067335},
doi = {10.1504/IJBRA.2015.067335},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijbra/VaidyaP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ZhouZNM15,
author = {Ping Zhou and
Ning Zhang and
Ruth Nussinov and
Buyong Ma},
title = {Defining the Domain Arrangement of the Mammalian Target of Rapamycin
Complex Component Rictor Protein},
journal = {J. Comput. Biol.},
volume = {22},
number = {9},
pages = {876--886},
year = {2015},
url = {https://doi.org/10.1089/cmb.2015.0103},
doi = {10.1089/CMB.2015.0103},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/ZhouZNM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/DuffyODMOS15,
author = {Fergal J. Duffy and
Darragh O'Donovan and
Marc Devocelle and
Niamh Moran and
David J. O'Connell and
Denis C. Shields},
title = {Virtual Screening Using Combinatorial Cyclic Peptide Libraries Reveals
Protein Interfaces Readily Targetable by Cyclic Peptides},
journal = {J. Chem. Inf. Model.},
volume = {55},
number = {3},
pages = {600--613},
year = {2015},
url = {https://doi.org/10.1021/ci500431q},
doi = {10.1021/CI500431Q},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/DuffyODMOS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/RooklinWKAZ15,
author = {David Rooklin and
Cheng Wang and
Joseph Katigbak and
Paramjit S. Arora and
Yingkai Zhang},
title = {AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein-Protein
Interaction Interfaces},
journal = {J. Chem. Inf. Model.},
volume = {55},
number = {8},
pages = {1585--1599},
year = {2015},
url = {https://doi.org/10.1021/acs.jcim.5b00103},
doi = {10.1021/ACS.JCIM.5B00103},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/RooklinWKAZ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SawadaIMY15,
author = {Ryusuke Sawada and
Hiroaki Iwata and
Sayaka Mizutani and
Yoshihiro Yamanishi},
title = {Target-Based Drug Repositioning Using Large-Scale Chemical-Protein
Interactome Data},
journal = {J. Chem. Inf. Model.},
volume = {55},
number = {12},
pages = {2717--2730},
year = {2015},
url = {https://doi.org/10.1021/acs.jcim.5b00330},
doi = {10.1021/ACS.JCIM.5B00330},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/SawadaIMY15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jsjkx/XieLZ18,
author = {Qianqian Xie and
Dingfang Li and
Wen Zhang},
title = {{\unicode{22522}}{\unicode{20110}}{\unicode{38598}}{\unicode{25104}}{\unicode{23398}}{\unicode{20064}}{\unicode{30340}}{\unicode{31163}}{\unicode{23376}}{\unicode{36890}}{\unicode{36947}}{\unicode{33647}}{\unicode{29289}}{\unicode{38774}}{\unicode{28857}}{\unicode{39044}}{\unicode{27979}}
(Predicting Potential Drug Targets from Ion Channel Proteins Based
on Ensemble Learning)},
journal = {{\unicode{35745}}{\unicode{31639}}{\unicode{26426}}{\unicode{31185}}{\unicode{23398}}},
volume = {42},
number = {4},
pages = {177--180},
year = {2015},
url = {https://doi.org/10.11896/j.issn.1002-137X.2015.04.035},
doi = {10.11896/J.ISSN.1002-137X.2015.04.035},
timestamp = {Mon, 27 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jsjkx/XieLZ18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ItoIYMT15,
author = {Jun{-}Ichi Ito and
Kazuyoshi Ikeda and
Kazunori D. Yamada and
Kenji Mizuguchi and
Kentaro Tomii},
title = {PoSSuM v.2.0: data update and a new function for investigating ligand
analogs and target proteins of small-molecule drugs},
journal = {Nucleic Acids Res.},
volume = {43},
number = {Database-Issue},
pages = {392--398},
year = {2015},
url = {https://doi.org/10.1093/nar/gku1144},
doi = {10.1093/NAR/GKU1144},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ItoIYMT15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pc/VasseurBSVMKD15,
author = {Romain Vasseur and
St{\'{e}}phanie Baud and
Luiz Angelo Steffenel and
Xavier Vigouroux and
Laurent Martiny and
Micha{\"{e}}l Krajecki and
Manuel Dauchez},
title = {Inverse docking method for new proteins targets identification: {A}
parallel approach},
journal = {Parallel Comput.},
volume = {42},
pages = {48--59},
year = {2015},
url = {https://doi.org/10.1016/j.parco.2014.09.008},
doi = {10.1016/J.PARCO.2014.09.008},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pc/VasseurBSVMKD15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/ManiCOMUB15,
author = {Subramani Mani and
Daniel Cannon and
Tudor I. Oprea and
Stephen L. Mathias and
Oleg Ursu and
Cristian Bologa},
title = {Protein Drug Target Prioritization for Illumination},
booktitle = {{AMIA} 2015, American Medical Informatics Association Annual Symposium,
San Francisco, CA, USA, November 14-18, 2015},
publisher = {{AMIA}},
year = {2015},
url = {https://knowledge.amia.org/59310-amia-1.2741865/t001-1.2745946/f001-1.2745947/2247351-1.2746059/2248806-1.2746056},
timestamp = {Wed, 17 Apr 2024 11:47:40 +0200},
biburl = {https://dblp.org/rec/conf/amia/ManiCOMUB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cikm/KeumYN15,
author = {Jongsoo Keum and
Sunyong Yoo and
Hojung Nam},
editor = {Doheon Lee and
Min Song and
Karin Verspoor},
title = {Prediction of Compound-Target Interactions of Natural Products Using
Large-scale Drug and Protein Information},
booktitle = {Proceedings of the {ACM} Ninth International Workshop on Data and
Text Mining in Biomedical Informatics, {DTMBIO} 2015, Melbourne, Australia,
October 23, 2015},
pages = {15},
publisher = {{ACM}},
year = {2015},
url = {https://doi.org/10.1145/2811163.2811172},
doi = {10.1145/2811163.2811172},
timestamp = {Thu, 17 Feb 2022 16:43:16 +0100},
biburl = {https://dblp.org/rec/conf/cikm/KeumYN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/embc/RavinarayananPC15,
author = {Haribalaganesh Ravinarayanan and
Bibhash K. Paul and
Angshu Chakraborty and
Krishnan Sundar},
title = {Homology modeling of target proteins and identification novel antifungal
compounds against Candida tropicalis through structure based virtual
screening},
booktitle = {37th Annual International Conference of the {IEEE} Engineering in
Medicine and Biology Society, {EMBC} 2015, Milan, Italy, August 25-29,
2015},
pages = {4419--4422},
publisher = {{IEEE}},
year = {2015},
url = {https://doi.org/10.1109/EMBC.2015.7319375},
doi = {10.1109/EMBC.2015.7319375},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/embc/RavinarayananPC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/memea/ManfrediMPSRM15,
author = {Marcello Manfredi and
Simona Martinotti and
Mauro Patrone and
Maria Paola Sassi and
Elia Ranzato and
Emilio Marengo},
title = {Targeted quantitation of {HMGB1} protein by label-free Mass Spectrometry
technique},
booktitle = {2015 {IEEE} International Symposium on Medical Measurements and Applications,
MeMeA 2015, Torino, Italy, May 7-9, 2015},
pages = {526--530},
publisher = {{IEEE}},
year = {2015},
url = {https://doi.org/10.1109/MeMeA.2015.7145260},
doi = {10.1109/MEMEA.2015.7145260},
timestamp = {Wed, 16 Oct 2019 14:14:54 +0200},
biburl = {https://dblp.org/rec/conf/memea/ManfrediMPSRM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/alr/HaseKGKT14,
author = {Takeshi Hase and
Kaito Kikuchi and
Samik Ghosh and
Hiroaki Kitano and
Hiroshi Tanaka},
title = {Identification of drug-target modules in the human protein-protein
interaction network},
journal = {Artif. Life Robotics},
volume = {19},
number = {4},
pages = {406--413},
year = {2014},
url = {https://doi.org/10.1007/s10015-014-0178-5},
doi = {10.1007/S10015-014-0178-5},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/alr/HaseKGKT14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YangSSK14,
author = {Jae{-}Seong Yang and
Eduard Sabid{\'{o}} and
Luis Serrano and
Christina Kiel},
title = {{TAPAS:} tools to assist the targeted protein quantification of human
alternative splice variants},
journal = {Bioinform.},
volume = {30},
number = {20},
pages = {2989--2990},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu428},
doi = {10.1093/BIOINFORMATICS/BTU428},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YangSSK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/FadhalMG14,
author = {Emad Fadhal and
Eric C. Mwambene and
Junaid Gamieldien},
title = {Modelling human protein interaction networks as metric spaces has
potential in disease research and drug target discovery},
journal = {{BMC} Syst. Biol.},
volume = {8},
pages = {68},
year = {2014},
url = {https://doi.org/10.1186/1752-0509-8-68},
doi = {10.1186/1752-0509-8-68},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcsb/FadhalMG14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/WangLTX14,
author = {Jiao T. Wang and
Wei Liu and
Hailin Tang and
Hongwei Xie},
title = {Screening drug target proteins based on sequence information},
journal = {J. Biomed. Informatics},
volume = {49},
pages = {269--274},
year = {2014},
url = {https://doi.org/10.1016/j.jbi.2014.03.009},
doi = {10.1016/J.JBI.2014.03.009},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/WangLTX14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Khan14,
author = {Abdul Arif Khan},
title = {\emph{In Silico} Prediction of \emph{Escherichia coli} Proteins Targeting
the Host Cell Nucleus, with Special Reference to Their Role in Colon
Cancer Etiology},
journal = {J. Comput. Biol.},
volume = {21},
number = {6},
pages = {466--475},
year = {2014},
url = {https://doi.org/10.1089/cmb.2014.0001},
doi = {10.1089/CMB.2014.0001},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/Khan14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LarsenWJV14,
author = {Adrien B. Larsen and
Jeffrey R. Wagner and
Abhinandan Jain and
Nagarajan Vaidehi},
title = {Protein Structure Refinement of {CASP} Target Proteins Using {GNEIMO}
Torsional Dynamics Method},
journal = {J. Chem. Inf. Model.},
volume = {54},
number = {2},
pages = {508--517},
year = {2014},
url = {https://doi.org/10.1021/ci400484c},
doi = {10.1021/CI400484C},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/LarsenWJV14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LiKTSV14,
author = {Hubert Li and
Vinod Kasam and
Christofer S. Tautermann and
Daniel Seeliger and
Nagarajan Vaidehi},
title = {Computational Method To Identify Druggable Binding Sites That Target
Protein-Protein Interactions},
journal = {J. Chem. Inf. Model.},
volume = {54},
number = {5},
pages = {1391--1400},
year = {2014},
url = {https://doi.org/10.1021/ci400750x},
doi = {10.1021/CI400750X},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/LiKTSV14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/Sugaya14,
author = {Nobuyoshi Sugaya},
title = {Ligand Efficiency-Based Support Vector Regression Models for Predicting
Bioactivities of Ligands to Drug Target Proteins},
journal = {J. Chem. Inf. Model.},
volume = {54},
number = {10},
pages = {2751--2763},
year = {2014},
url = {https://doi.org/10.1021/ci5003262},
doi = {10.1021/CI5003262},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/Sugaya14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/TianSPLZLH14,
author = {Sheng Tian and
Huiyong Sun and
Peichen Pan and
Dan Li and
Xuechu Zhen and
Youyong Li and
Tingjun Hou},
title = {Assessing an Ensemble Docking-Based Virtual Screening Strategy for
Kinase Targets by Considering Protein Flexibility},
journal = {J. Chem. Inf. Model.},
volume = {54},
number = {10},
pages = {2664--2679},
year = {2014},
url = {https://doi.org/10.1021/ci500414b},
doi = {10.1021/CI500414B},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/TianSPLZLH14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/netmahib/SagarPPSPG14,
author = {Mamta Sagar and
Rajesh Kumar Pathak and
Rishi Kumar Pandey and
Dev Bukhsh Singh and
Neetesh Pandey and
Manish Kumar Gupta},
title = {Binding affinity analysis and {ADMET} prediction of epigallocatechine
gallate {(EGCG)} derivatives for {AP-1} protein: a drug target for
liver cancer},
journal = {Netw. Model. Anal. Health Informatics Bioinform.},
volume = {3},
number = {1},
year = {2014},
url = {https://doi.org/10.1007/s13721-014-0066-x},
doi = {10.1007/S13721-014-0066-X},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/netmahib/SagarPPSPG14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/BarreraAMCV14,
author = {Alejandro Barrera and
Ana Alastruey{-}Izquierdo and
Mar{\'{\i}}a J. Mart{\'{\i}}n and
Isabel Cuesta and
Juan Antonio Vizca{\'{\i}}no},
title = {Analysis of the Protein Domain and Domain Architecture Content in
Fungi and Its Application in the Search of New Antifungal Targets},
journal = {PLoS Comput. Biol.},
volume = {10},
number = {7},
year = {2014},
url = {https://doi.org/10.1371/journal.pcbi.1003733},
doi = {10.1371/JOURNAL.PCBI.1003733},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/BarreraAMCV14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ChuLMWSWHW14,
author = {Xiakun Chu and
Fei Liu and
Brian A. Maxwell and
Yong Wang and
Zucai Suo and
Haijun Wang and
Wei Han and
Jin Wang},
title = {Dynamic Conformational Change Regulates the Protein-DNA Recognition:
An Investigation on Binding of a Y-Family Polymerase to Its Target
{DNA}},
journal = {PLoS Comput. Biol.},
volume = {10},
number = {9},
year = {2014},
url = {https://doi.org/10.1371/journal.pcbi.1003804},
doi = {10.1371/JOURNAL.PCBI.1003804},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/ChuLMWSWHW14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/tr/Aras13,
author = {Billur Engin},
title = {A novel structural protein-protein interaction network model: Its
applications on drug off-target prediction and genotype-phenotype
linkage (Yeni bir yap{\i}sal protein-protein etkile{\c{s}}imi a{\u{g}}
modeli: Bu modelin ila{\c{c}} uzak-hedeflerinin tahmininde ve genotip-fenotip
ba{\u{g}}lant{\i}s{\i} kurmaktaki uygulamalar{\i})},
school = {Ko{\c{c}} University, Turkey},
year = {2013},
url = {https://tez.yok.gov.tr/UlusalTezMerkezi/tezDetay.jsp?id=-bD-GrIYxXlupeB-LCkf2Q\&no=CxTHxyw6RHLoIQzn50reEw},
timestamp = {Sun, 29 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/phd/tr/Aras13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BergeyWA13,
author = {Christina M. Bergey and
Andrew M. Watkins and
Paramjit S. Arora},
title = {HippDB: a database of readily targeted helical protein-protein interactions},
journal = {Bioinform.},
volume = {29},
number = {21},
pages = {2806--2807},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt483},
doi = {10.1093/BIOINFORMATICS/BTT483},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BergeyWA13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/IndioMSFC13,
author = {Valentina Indio and
Pier Luigi Martelli and
Castrense Savojardo and
Piero Fariselli and
Rita Casadio},
title = {The prediction of organelle-targeting peptides in eukaryotic proteins
with Grammatical-Restrained Hidden Conditional Random Fields},
journal = {Bioinform.},
volume = {29},
number = {8},
pages = {981--988},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt089},
doi = {10.1093/BIOINFORMATICS/BTT089},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/IndioMSFC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/IwataMTKGY13,
author = {Hiroaki Iwata and
Sayaka Mizutani and
Yasuo Tabei and
Masaaki Kotera and
Susumu Goto and
Yoshihiro Yamanishi},
title = {Inferring protein domains associated with drug side effects based
on drug-target interaction network},
journal = {{BMC} Syst. Biol.},
volume = {7},
number = {{S-6}},
pages = {S18},
year = {2013},
url = {https://doi.org/10.1186/1752-0509-7-S6-S18},
doi = {10.1186/1752-0509-7-S6-S18},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/IwataMTKGY13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijmei/LathaAKN13,
author = {A. Ashretha Latha and
V. Aarthi and
M. Surendher Kumar and
R. B. Narayanan},
title = {Capsid protein from Indian isolate of chikungunya virus as a possible
drug target: an in silico study},
journal = {Int. J. Medical Eng. Informatics},
volume = {5},
number = {3},
pages = {223--232},
year = {2013},
url = {https://doi.org/10.1504/IJMEI.2013.055688},
doi = {10.1504/IJMEI.2013.055688},
timestamp = {Mon, 11 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijmei/LathaAKN13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/Cortes-CirianoKABV13,
author = {Isidro Cortes{-}Ciriano and
Alexios Koutsoukas and
Olga Abian and
Andreas Bender and
Adri{\'{a}}n Vel{\'{a}}zquez{-}Campoy},
title = {Experimental validation of in silico target predictions on synergistic
protein targets},
journal = {J. Cheminformatics},
volume = {5},
number = {{S-1}},
pages = {31},
year = {2013},
url = {https://doi.org/10.1186/1758-2946-5-S1-P31},
doi = {10.1186/1758-2946-5-S1-P31},
timestamp = {Wed, 13 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/Cortes-CirianoKABV13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/MavridisM13,
author = {Lazaros Mavridis and
John B. O. Mitchell},
title = {Predicting the protein targets for athletic performance-enhancing
substances},
journal = {J. Cheminformatics},
volume = {5},
pages = {31},
year = {2013},
url = {https://doi.org/10.1186/1758-2946-5-31},
doi = {10.1186/1758-2946-5-31},
timestamp = {Thu, 14 Feb 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/MavridisM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/Wade13,
author = {Rebecca C. Wade},
title = {Targeting protein dynamics in drug design},
journal = {J. Cheminformatics},
volume = {5},
number = {{S-1}},
pages = {1},
year = {2013},
url = {https://doi.org/10.1186/1758-2946-5-S1-O1},
doi = {10.1186/1758-2946-5-S1-O1},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/Wade13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/MetzSGWG13,
author = {Alexander Metz and
Julia Schanda and
Manuel Grez and
Christian Wichmann and
Holger Gohlke},
title = {From Determinants of {RUNX1/ETO} Tetramerization to Small-Molecule
Protein-Protein Interaction Inhibitors Targeting Acute Myeloid Leukemia},
journal = {J. Chem. Inf. Model.},
volume = {53},
number = {9},
pages = {2197--2202},
year = {2013},
url = {https://doi.org/10.1021/ci400332e},
doi = {10.1021/CI400332E},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/MetzSGWG13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/NguyenLPSVS13,
author = {Kong T. Nguyen and
Fengling Li and
Gennadiy Poda and
David Smil and
Masoud Vedadi and
Matthieu Schapira},
title = {Strategy to Target the Substrate Binding site of {SET} Domain Protein
Methyltransferases},
journal = {J. Chem. Inf. Model.},
volume = {53},
number = {3},
pages = {681--691},
year = {2013},
url = {https://doi.org/10.1021/ci300596x},
doi = {10.1021/CI300596X},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/NguyenLPSVS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/Sugaya13,
author = {Nobuyoshi Sugaya},
title = {Training Based on Ligand Efficiency Improves Prediction of Bioactivities
of Ligands and Drug Target Proteins in a Machine Learning Approach},
journal = {J. Chem. Inf. Model.},
volume = {53},
number = {10},
pages = {2525--2537},
year = {2013},
url = {https://doi.org/10.1021/ci400240u},
doi = {10.1021/CI400240U},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/Sugaya13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/EichbornDGPHBASANCGNSP13,
author = {Joachim von Eichborn and
Mathias Dunkel and
Bj{\"{o}}rn O. Gohlke and
Sarah C. Preissner and
Michael F. Hoffmann and
Jakob M. J. Bauer and
J. Douglas Armstrong and
Martin H. Schaefer and
Miguel A. Andrade{-}Navarro and
Nicolas Le Nov{\`{e}}re and
Michael D. R. Croning and
Seth G. N. Grant and
Pim van Nierop and
August B. Smit and
Robert Preissner},
title = {SynSysNet: integration of experimental data on synaptic protein-protein
interactions with drug-target relations},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Database-Issue},
pages = {834--840},
year = {2013},
url = {https://doi.org/10.1093/nar/gks1040},
doi = {10.1093/NAR/GKS1040},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/EichbornDGPHBASANCGNSP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ZulawskiBS13,
author = {Monika Zulawski and
Rostyslav Braginets and
Waltraud X. Schulze},
title = {PhosPhAt goes kinases - searchable protein kinase target information
in the plant phosphorylation site database PhosPhAt},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Database-Issue},
pages = {1176--1184},
year = {2013},
url = {https://doi.org/10.1093/nar/gks1081},
doi = {10.1093/NAR/GKS1081},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ZulawskiBS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/RobertsonHTCBVGMB13,
author = {James C. Robertson and
Nate C. Hurley and
Marcello Tortorici and
Giuseppe Ciossani and
Maria Teresa Borrello and
Nadeem A. Vellore and
A. Ganesan and
Andrea Mattevi and
Riccardo Baron},
title = {Expanding the Druggable Space of the LSD1/CoREST Epigenetic Target:
New Potential Binding Regions for Drug-Like Molecules, Peptides, Protein
Partners, and Chromatin},
journal = {PLoS Comput. Biol.},
volume = {9},
number = {7},
year = {2013},
url = {https://doi.org/10.1371/journal.pcbi.1003158},
doi = {10.1371/JOURNAL.PCBI.1003158},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/RobertsonHTCBVGMB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/YuHYSTY13,
author = {Dong{-}Jun Yu and
Jun Hu and
Jing Yang and
Hong{-}Bin Shen and
Jinhui Tang and
Jing{-}Yu Yang},
title = {Designing Template-Free Predictor for Targeting Protein-Ligand Binding
Sites with Classifier Ensemble and Spatial Clustering},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {10},
number = {4},
pages = {994--1008},
year = {2013},
url = {https://doi.org/10.1109/TCBB.2013.104},
doi = {10.1109/TCBB.2013.104},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/YuHYSTY13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/SantosSCL13,
author = {Eduardo Campos dos Santos and
Marcos Augusto dos Santos and
Br{\'{a}}ulio Roberto Gon{\c{c}}alves Marinho Couto and
Julio Cesar Dias Lopes},
editor = {Pedro Fernandes and
Jordi Sol{\'{e}}{-}Casals and
Ana L. N. Fred and
Hugo Gamboa},
title = {A Semantic-based Similarity of Human Drug Target Proteins},
booktitle = {{BIOINFORMATICS} 2013 - Proceedings of the International Conference
on Bioinformatics Models, Methods and Algorithms, Barcelona, Spain,
11 - 14 February, 2013},
pages = {300--303},
publisher = {SciTePress},
year = {2013},
timestamp = {Tue, 01 Oct 2013 18:44:42 +0200},
biburl = {https://dblp.org/rec/conf/biostec/SantosSCL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/AshtawyM13,
author = {Hossam M. Ashtawy and
Nihar R. Mahapatra},
editor = {Zhipeng Cai and
Oliver Eulenstein and
Daniel Janies and
Daniel Schwartz},
title = {Does Accurate Scoring of Ligands against Protein Targets Mean Accurate
Ranking?},
booktitle = {Bioinformatics Research and Applications, 9th International Symposium,
{ISBRA} 2013, Charlotte, NC, USA, May 20-22, 2013. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7875},
pages = {298--310},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-38036-5\_29},
doi = {10.1007/978-3-642-38036-5\_29},
timestamp = {Thu, 20 Aug 2020 15:56:19 +0200},
biburl = {https://dblp.org/rec/conf/isbra/AshtawyM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/kse/TranNCP13,
author = {Dang Hung Tran and
Thanh{-}Phuong Nguyen and
Laura Caberlotto and
Corrado Priami},
editor = {Van{-}Nam Huynh and
Thierry Denoeux and
Dang Hung Tran and
Anh{-}Cuong Le and
Son Bao Pham},
title = {Inference of Autism-Related Genes by Integrating Protein-Protein Interactions
and miRNA-Target Interactions},
booktitle = {Knowledge and Systems Engineering - Proceedings of the Fifth International
Conference, {KSE} 2013, Volume 1, Hanoi, Vietnam, 17-19 October, 2013},
series = {Advances in Intelligent Systems and Computing},
volume = {244},
pages = {299--311},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-319-02741-8\_26},
doi = {10.1007/978-3-319-02741-8\_26},
timestamp = {Sat, 16 Sep 2017 12:10:18 +0200},
biburl = {https://dblp.org/rec/conf/kse/TranNCP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/dnb/Lee12,
author = {Hang{-}mao Lee},
title = {Bioinformatics pre-selection of thioredoxin/glutaredoxin target proteins
for the construction of cellular redox regulatory network},
school = {Bielefeld University},
year = {2012},
url = {http://pub.uni-bielefeld.de/publication/2515632},
urn = {urn:nbn:de:hbz:361-25156321},
timestamp = {Sat, 17 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/phd/dnb/Lee12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ReczkoMAGH12,
author = {Martin Reczko and
Manolis Maragkakis and
Panagiotis Alexiou and
Ivo Grosse and
Artemis G. Hatzigeorgiou},
title = {Functional microRNA targets in protein coding sequences},
journal = {Bioinform.},
volume = {28},
number = {6},
pages = {771--776},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts043},
doi = {10.1093/BIOINFORMATICS/BTS043},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ReczkoMAGH12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MoraD12,
author = {Antonio Mora and
Ian M. Donaldson},
title = {Effects of protein interaction data integration, representation and
reliability on the use of network properties for drug target prediction},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {294},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-294},
doi = {10.1186/1471-2105-13-294},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MoraD12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TerraponGMB12,
author = {Nicolas Terrapon and
Olivier Gascuel and
Eric Mar{\'{e}}chal and
Laurent Br{\'{e}}h{\'{e}}lin},
title = {Fitting hidden Markov models of protein domains to a target species:
application to Plasmodium falciparum},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {67},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-67},
doi = {10.1186/1471-2105-13-67},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/TerraponGMB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/McDermottDCRKW12,
author = {Jason E. McDermott and
Deborah L. Diamond and
Courtney D. Corley and
Angela L. Rasmussen and
Michael G. Katze and
Katrina M. Waters},
title = {Topological analysis of protein co-abundance networks identifies novel
host targets important for {HCV} infection and pathogenesis},
journal = {{BMC} Syst. Biol.},
volume = {6},
pages = {28},
year = {2012},
url = {https://doi.org/10.1186/1752-0509-6-28},
doi = {10.1186/1752-0509-6-28},
timestamp = {Fri, 19 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/McDermottDCRKW12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijdmb/ShuHZ12,
author = {Gang Shu and
Xiaodi Huang and
Shanfeng Zhu},
title = {A consensus method for prioritising drug-associated target proteins},
journal = {Int. J. Data Min. Bioinform.},
volume = {6},
number = {2},
pages = {178--195},
year = {2012},
url = {https://doi.org/10.1504/IJDMB.2012.048197},
doi = {10.1504/IJDMB.2012.048197},
timestamp = {Mon, 11 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijdmb/ShuHZ12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/VinhSSC12,
author = {Natalie B. Vinh and
Jamie S. Simpson and
Peter J. Scammells and
David K. Chalmers},
title = {Virtual screening using a conformationally flexible target protein:
models for ligand binding to p38{\(\alpha\)} {MAPK}},
journal = {J. Comput. Aided Mol. Des.},
volume = {26},
number = {4},
pages = {409--423},
year = {2012},
url = {https://doi.org/10.1007/s10822-012-9569-7},
doi = {10.1007/S10822-012-9569-7},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/VinhSSC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/Cherkasov12,
author = {Artem Cherkasov},
title = {Targeting protein-protein interactions using methods of cheminformatics},
journal = {J. Cheminformatics},
volume = {4},
number = {{S-1}},
pages = {3},
year = {2012},
url = {https://doi.org/10.1186/1758-2946-4-S1-P3},
doi = {10.1186/1758-2946-4-S1-P3},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/Cherkasov12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/ScharfePS12,
author = {Michael Scharfe and
Martin Pippel and
Wolfgang Sippl},
title = {Development of target-biased scoring functions for protein-ligand
docking},
journal = {J. Cheminformatics},
volume = {4},
number = {{S-1}},
pages = {35},
year = {2012},
url = {https://doi.org/10.1186/1758-2946-4-S1-P35},
doi = {10.1186/1758-2946-4-S1-P35},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/ScharfePS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/EnginKNG12,
author = {Billur Engin and
Ozlem Keskin and
Ruth Nussinov and
Attila G{\"{u}}rsoy},
title = {A Strategy Based on Protein-Protein Interface Motifs May Help in Identifying
Drug Off-Targets},
journal = {J. Chem. Inf. Model.},
volume = {52},
number = {8},
pages = {2273--2286},
year = {2012},
url = {https://doi.org/10.1021/ci300072q},
doi = {10.1021/CI300072Q},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/EnginKNG12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jclinbioinf/ZhaoWWH12,
author = {Yuqi Zhao and
Jingwen Wang and
Yanjie Wang and
Jingfei Huang},
title = {A comparative analysis of protein targets of withdrawn cardiovascular
drugs in human and mouse},
journal = {J. Clin. Bioinform.},
volume = {2},
pages = {10},
year = {2012},
url = {https://doi.org/10.1186/2043-9113-2-10},
doi = {10.1186/2043-9113-2-10},
timestamp = {Thu, 02 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jclinbioinf/ZhaoWWH12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/WangCCL12,
author = {Jui{-}Chih Wang and
Pei{-}Ying Chu and
Chung{-}Ming Chen and
Jung{-}Hsin Lin},
title = {idTarget: a web server for identifying protein targets of small chemical
molecules with robust scoring functions and a divide-and-conquer docking
approach},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Web-Server-Issue},
pages = {393--399},
year = {2012},
url = {https://doi.org/10.1093/nar/gks496},
doi = {10.1093/NAR/GKS496},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/WangCCL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/KrugerO12,
author = {Felix A. Kr{\"{u}}ger and
John P. Overington},
title = {Global Analysis of Small Molecule Binding to Related Protein Targets},
journal = {PLoS Comput. Biol.},
volume = {8},
number = {1},
year = {2012},
url = {https://doi.org/10.1371/journal.pcbi.1002333},
doi = {10.1371/JOURNAL.PCBI.1002333},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/KrugerO12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/ZhangLH12,
author = {Jintao Zhang and
Gerald H. Lushington and
Jun Huan},
editor = {Sanjay Ranka and
Tamer Kahveci and
Mona Singh},
title = {Multi-target protein-chemical interaction prediction using task-regularized
and boosted multi-task learning},
booktitle = {{ACM} International Conference on Bioinformatics, Computational Biology
and Biomedicine, BCB' 12, Orlando, FL, {USA} - October 08 - 10, 2012},
pages = {60--67},
publisher = {{ACM}},
year = {2012},
url = {https://doi.org/10.1145/2382936.2382944},
doi = {10.1145/2382936.2382944},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/ZhangLH12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gensips/HaiderBPDK12,
author = {Saad Haider and
Noah Berlow and
Ranadip Pal and
Lara E. Davis and
Charles Keller},
title = {Combination therapy design for targeted therapeutics from a drug-protein
interaction perspective},
booktitle = {Proceedings 2012 {IEEE} International Workshop on Genomic Signal Processing
and Statistics, GENSiPS 2012, Washington, DC, USA, December 2-4, 2012},
pages = {58--61},
publisher = {{IEEE}},
year = {2012},
url = {https://doi.org/10.1109/GENSIPS.2012.6507726},
doi = {10.1109/GENSIPS.2012.6507726},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gensips/HaiderBPDK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ibica/HuangCZ12,
author = {Xiaofeng Huang and
Tongcheng Cao and
Guohua Zhao},
title = {Potential Protein Targets and Toxicological Mechanism of Persistent
Organic Polluntant Perfluorooctanesulfonate},
booktitle = {2012 Third International Conference on Innovations in Bio-Inspired
Computing and Applications, Kaohsiung City, Taiwan, September 26-28,
2012},
pages = {218--222},
publisher = {{IEEE}},
year = {2012},
url = {https://doi.org/10.1109/IBICA.2012.70},
doi = {10.1109/IBICA.2012.70},
timestamp = {Wed, 16 Oct 2019 14:14:56 +0200},
biburl = {https://dblp.org/rec/conf/ibica/HuangCZ12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipcat/ColingeRBS12,
author = {Jacques Colinge and
Uwe Rix and
Keiryn L. Bennett and
Giulio Superti{-}Furga},
editor = {Michael A. Lones and
Stephen L. Smith and
Sarah A. Teichmann and
Felix Naef and
James Alfred Walker and
Martin Trefzer},
title = {Systems Biology Analysis of Kinase Inhibitor Protein Target Profiles
in Leukemia Treatments},
booktitle = {Information Processign in Cells and Tissues - 9th International Conference,
{IPCAT} 2012, Cambridge, UK, March 31 - April 2, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7223},
pages = {62--66},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-28792-3\_9},
doi = {10.1007/978-3-642-28792-3\_9},
timestamp = {Thu, 23 Jun 2022 19:59:03 +0200},
biburl = {https://dblp.org/rec/conf/ipcat/ColingeRBS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HillAMKS11,
author = {Jonathon T. Hill and
Keith R. Anderson and
Teresa L. Mastracci and
Klaus H. Kaestner and
Lori Sussel},
title = {Novel computational analysis of protein binding microarray data identifies
direct targets of Nkx2.2 in the pancreas},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {62},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-62},
doi = {10.1186/1471-2105-12-62},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HillAMKS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/Wong11a,
author = {Limsoon Wong},
title = {Introduction - Some New Results and Tools for Protein Function Prediction,
{RNA} Target Site Prediction, Genotype Calling, Environmental Genomics,
and More},
journal = {J. Bioinform. Comput. Biol.},
volume = {9},
number = {6},
year = {2011},
url = {https://doi.org/10.1142/S021972001100580X},
doi = {10.1142/S021972001100580X},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/Wong11a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/GohlkeMPKK11,
author = {Holger Gohlke and
Alexander Metz and
Christopher Pfleger and
Dennis M. Kr{\"{u}}ger and
Sina Kazemi},
title = {Towards targeting protein-protein interfaces with small molecules},
journal = {J. Cheminformatics},
volume = {3},
number = {{S-1}},
pages = {21},
year = {2011},
url = {https://doi.org/10.1186/1758-2946-3-S1-O21},
doi = {10.1186/1758-2946-3-S1-O21},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/GohlkeMPKK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/SouthanBJM11,
author = {Christopher Southan and
Kiran Boppana and
Sarma A. R. P. Jagarlapudi and
Sorel Muresan},
title = {Analysis of in vitro bioactivity data extracted from drug discovery
literature and patents: Ranking 1654 human protein targets by assayed
compounds and molecular scaffolds},
journal = {J. Cheminformatics},
volume = {3},
pages = {14},
year = {2011},
url = {https://doi.org/10.1186/1758-2946-3-14},
doi = {10.1186/1758-2946-3-14},
timestamp = {Thu, 14 Feb 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/SouthanBJM11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/CalvaresiZ11,
author = {Matteo Calvaresi and
Francesco Zerbetto},
title = {In Silico Carborane Docking to Proteins and Potential Drug Targets},
journal = {J. Chem. Inf. Model.},
volume = {51},
number = {8},
pages = {1882--1896},
year = {2011},
url = {https://doi.org/10.1021/ci200216z},
doi = {10.1021/CI200216Z},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/CalvaresiZ11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FuchsSJBKWL11,
author = {Julian E. Fuchs and
Gudrun M. Spitzer and
Ameera Javed and
Adam Biela and
Christoph Kreutz and
Bernd Wellenzohn and
Klaus R. Liedl},
title = {Minor Groove Binders and Drugs Targeting Proteins Cover Complementary
Regions in Chemical Shape Space},
journal = {J. Chem. Inf. Model.},
volume = {51},
number = {9},
pages = {2223--2232},
year = {2011},
url = {https://doi.org/10.1021/ci200237c},
doi = {10.1021/CI200237C},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/FuchsSJBKWL11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/KinningsJ11,
author = {Sarah L. Kinnings and
Richard M. Jackson},
title = {ReverseScreen3D: {A} Structure-Based Ligand Matching Method To Identify
Protein Targets},
journal = {J. Chem. Inf. Model.},
volume = {51},
number = {3},
pages = {624--634},
year = {2011},
url = {https://doi.org/10.1021/ci1003174},
doi = {10.1021/CI1003174},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/KinningsJ11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/Perez-NuenoR11,
author = {Violeta I. P{\'{e}}rez{-}Nueno and
David W. Ritchie},
title = {Using Consensus-Shape Clustering To Identify Promiscuous Ligands and
Protein Targets and To Choose the Right Query for Shape-Based Virtual
Screening},
journal = {J. Chem. Inf. Model.},
volume = {51},
number = {6},
pages = {1233--1248},
year = {2011},
url = {https://doi.org/10.1021/ci100492r},
doi = {10.1021/CI100492R},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/Perez-NuenoR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SinghBJ11,
author = {Tanya Singh and
D. Biswas and
Bhyravabhotla Jayaram},
title = {\emph{AADS} - An Automated Active Site Identification, Docking, and
Scoring Protocol for Protein Targets Based on Physicochemical Descriptors},
journal = {J. Chem. Inf. Model.},
volume = {51},
number = {10},
pages = {2515--2527},
year = {2011},
url = {https://doi.org/10.1021/ci200193z},
doi = {10.1021/CI200193Z},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/SinghBJ11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/WangLWLZLZLZJ11,
author = {Fei Wang and
DongXiang Liu and
Heyao Wang and
Cheng Luo and
Mingyue Zheng and
Hong Liu and
Weiliang Zhu and
Xiaomin Luo and
Jian Zhang and
Hualiang Jiang},
title = {Computational Screening for Active Compounds Targeting Protein Sequences:
Methodology and Experimental Validation},
journal = {J. Chem. Inf. Model.},
volume = {51},
number = {11},
pages = {2821--2828},
year = {2011},
url = {https://doi.org/10.1021/ci200264h},
doi = {10.1021/CI200264H},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/WangLWLZLZLZJ11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/YamanishiPSS11,
author = {Yoshihiro Yamanishi and
Edouard Pauwels and
Hiroto Saigo and
V{\'{e}}ronique Stoven},
title = {Extracting Sets of Chemical Substructures and Protein Domains Governing
Drug-Target Interactions},
journal = {J. Chem. Inf. Model.},
volume = {51},
number = {5},
pages = {1183--1194},
year = {2011},
url = {https://doi.org/10.1021/ci100476q},
doi = {10.1021/CI100476Q},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/YamanishiPSS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/GuptaMZLW11,
author = {Ankit Gupta and
Xiangdong Meng and
Lihua Julie Zhu and
Nathan D. Lawson and
Scot A. Wolfe},
title = {Zinc finger protein-dependent and -independent contributions to the
\emph{in vivo} off-target activity of zinc finger nucleases},
journal = {Nucleic Acids Res.},
volume = {39},
number = {1},
pages = {381--392},
year = {2011},
url = {https://doi.org/10.1093/nar/gkq787},
doi = {10.1093/NAR/GKQ787},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/GuptaMZLW11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/KalininaWAR11,
author = {Olga V. Kalinina and
Oliver Wichmann and
Gordana Apic and
Robert B. Russell},
title = {Combinations of Protein-Chemical Complex Structures Reveal New Targets
for Established Drugs},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {5},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1002043},
doi = {10.1371/JOURNAL.PCBI.1002043},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/KalininaWAR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/MeszarosTVDS11,
author = {B{\'{a}}lint M{\'{e}}sz{\'{a}}ros and
Judit T{\'{o}}th and
Be{\'{a}}ta G. V{\'{e}}rtessy and
Zsuzsanna Doszt{\'{a}}nyi and
Istv{\'{a}}n Simon},
title = {Proteins with Complex Architecture as Potential Targets for Drug Design:
{A} Case Study of \emph{Mycobacterium tuberculosi}s},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {7},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1002118},
doi = {10.1371/JOURNAL.PCBI.1002118},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/MeszarosTVDS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/WangWCHHW11,
author = {Jin Wang and
Yong Wang and
Xiakun Chu and
Stephen J. Hagen and
Wei Han and
Erkang Wang},
title = {Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically
Disordered Protein Inhibitor {IA3} to its Target Enzyme},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {4},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1001118},
doi = {10.1371/JOURNAL.PCBI.1001118},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/WangWCHHW11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/YangWCJLSWGQHFH11,
author = {Lun Yang and
Kejian Wang and
Jian Chen and
Anil G. Jegga and
Heng Luo and
Leming Shi and
Chunling Wan and
Xizhi Guo and
Shengying Qin and
Guang He and
Guoyin Feng and
Lin He},
title = {Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via
Chemical-Protein Interactome - Clozapine-Induced Agranulocytosis as
a Case Study},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {3},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1002016},
doi = {10.1371/JOURNAL.PCBI.1002016},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/YangWCJLSWGQHFH11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gensips/NguyenZWHJSLCL11,
author = {Nguyen T. Nguyen and
Xiaolin Zhang and
Yunji Wang and
Hai{-}Chao Han and
Yufang Jin and
Galen Schmidt and
Richard A. Lange and
Robert J. Chilton and
Merry Lindsey},
title = {Targeting myocardial infarction-specific protein interaction network
using computational analyses},
booktitle = {2011 {IEEE} International Workshop on Genomic Signal Processing and
Statistics, GENSiPS 2011, San Antonio, TX, USA, December 4-6, 2011},
pages = {198--201},
publisher = {{IEEE}},
year = {2011},
url = {https://doi.org/10.1109/GENSiPS.2011.6169479},
doi = {10.1109/GENSIPS.2011.6169479},
timestamp = {Wed, 16 Oct 2019 14:14:54 +0200},
biburl = {https://dblp.org/rec/conf/gensips/NguyenZWHJSLCL11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FlorezPBKKMEM10,
author = {Andr{\'{e}}s F. Fl{\'{o}}rez and
Daeui Park and
Jong Bhak and
Byoung{-}Chul Kim and
Allan Kuchinsky and
John H. Morris and
Jairo Espinosa and
Carlos Muskus},
title = {Protein network prediction and topological analysis in \emph{Leishmania
major }as a tool for drug target selection},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {484},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-484},
doi = {10.1186/1471-2105-11-484},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/FlorezPBKKMEM10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LamKMTSTSG10,
author = {Hugo Y. K. Lam and
Philip M. Kim and
Janine Mok and
Raffi Tonikian and
Sachdev S. Sidhu and
Benjamin E. Turk and
Michael Snyder and
Mark B. Gerstein},
title = {{MOTIPS:} Automated Motif Analysis for Predicting Targets of Modular
Protein Domains},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {243},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-243},
doi = {10.1186/1471-2105-11-243},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LamKMTSTSG10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WuCCHN10,
author = {Timothy H. Wu and
Ian Chang and
Lichieh Julie Chu and
Hsuan{-}Cheng Huang and
Wailap V. Ng},
title = {Modularity of Escherichia coli sRNA regulation revealed by sRNA-target
and protein network analysis},
journal = {{BMC} Bioinform.},
volume = {11},
number = {{S-7}},
pages = {S11},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-S7-S11},
doi = {10.1186/1471-2105-11-S7-S11},
timestamp = {Fri, 30 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WuCCHN10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/JungbluthRT10,
author = {Marc Jungbluth and
Christian Renicke and
Christof Taxis},
title = {Targeted protein depletion in Saccharomyces cerevisiae by activation
of a bidirectional degron},
journal = {{BMC} Syst. Biol.},
volume = {4},
pages = {176},
year = {2010},
url = {https://doi.org/10.1186/1752-0509-4-176},
doi = {10.1186/1752-0509-4-176},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/JungbluthRT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/candc/AitaNH10,
author = {Takuyo Aita and
Koichi Nishigaki and
Yuzuru Husimi},
title = {Toward the fast blind docking of a peptide to a target protein by
using a four-body statistical pseudo-potential},
journal = {Comput. Biol. Chem.},
volume = {34},
number = {1},
pages = {53--62},
year = {2010},
url = {https://doi.org/10.1016/j.compbiolchem.2009.10.005},
doi = {10.1016/J.COMPBIOLCHEM.2009.10.005},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/candc/AitaNH10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijbra/AiZZSZLLZL10,
author = {Haixin Ai and
Fangliang Zheng and
Chunyu Zhu and
Tingting Sun and
Li Zhang and
Xue Liu and
Xuejiao Li and
Guangyu Zhu and
Hongsheng Liu},
title = {Discovery of novel influenza inhibitors targeting the interaction
of dsRNA with the {NS1} protein by structure-based virtual screening},
journal = {Int. J. Bioinform. Res. Appl.},
volume = {6},
number = {5},
pages = {449--460},
year = {2010},
url = {https://doi.org/10.1504/IJBRA.2010.037985},
doi = {10.1504/IJBRA.2010.037985},
timestamp = {Fri, 11 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijbra/AiZZSZLLZL10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/isb/ChakrabortyCARWHRS10,
author = {Sajib Chakraborty and
Rajib Chakravorty and
Musaddeque Ahmed and
Atiqur Rahman and
T. M. Zaved Waise and
Faizule Hassan and
Mustafizur Rahman and
Sohel Shamsuzzaman},
title = {A Computational Approach for Identification of Epitopes in Dengue
Virus Envelope Protein: {A} Step Towards Designing a Universal Dengue
Vaccine Targeting Endemic Regions},
journal = {Silico Biol.},
volume = {10},
number = {5-6},
pages = {235--246},
year = {2010},
url = {https://doi.org/10.3233/ISB-2010-0435},
doi = {10.3233/ISB-2010-0435},
timestamp = {Thu, 20 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/isb/ChakrabortyCARWHRS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/HormozdiariSBS10,
author = {Fereydoun Hormozdiari and
Raheleh Salari and
Vineet Bafna and
S{\"{u}}leyman Cenk Sahinalp},
title = {Protein-Protein Interaction Network Evaluation for Identifying Potential
Drug Targets},
journal = {J. Comput. Biol.},
volume = {17},
number = {5},
pages = {669--684},
year = {2010},
url = {https://doi.org/10.1089/cmb.2009.0032},
doi = {10.1089/CMB.2009.0032},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/HormozdiariSBS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/KochJFS10,
author = {Oliver Koch and
Timo J{\"{a}}ger and
Leopold Floh{\'{e}} and
Paul M. Selzer},
title = {Virtual screening by high-throughput docking using hydrogen bonding
constraints for targeting a protein-protein interface in M. tuberculosis},
journal = {J. Cheminformatics},
volume = {2},
number = {{S-1}},
pages = {24},
year = {2010},
url = {https://doi.org/10.1186/1758-2946-2-S1-P24},
doi = {10.1186/1758-2946-2-S1-P24},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/KochJFS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LiSSLLT10,
author = {Yaozong Li and
Jie Shen and
Xianqiang Sun and
Weihua Li and
Guixia Liu and
Yun Tang},
title = {Accuracy Assessment of Protein-Based Docking Programs against {RNA}
Targets},
journal = {J. Chem. Inf. Model.},
volume = {50},
number = {6},
pages = {1134--1146},
year = {2010},
url = {https://doi.org/10.1021/ci9004157},
doi = {10.1021/CI9004157},
timestamp = {Tue, 27 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/LiSSLLT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/MukherjeeDZA10,
author = {Prasenjit Mukherjee and
Prashant V. Desai and
Yu{-}Dong Zhou and
Mitchell A. Avery},
title = {Targeting the {BH3} Domain Mediated Protein-Protein Interaction of
Bcl-xL through Virtual Screening},
journal = {J. Chem. Inf. Model.},
volume = {50},
number = {5},
pages = {906--923},
year = {2010},
url = {https://doi.org/10.1021/ci1000373},
doi = {10.1021/CI1000373},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/MukherjeeDZA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SheridanMHCG10,
author = {Robert P. Sheridan and
Vladimir N. Maiorov and
M. Katharine Holloway and
Wendy D. Cornell and
Ying{-}Duo Gao},
title = {Drug-like Density: {A} Method of Quantifying the "Bindability" of
a Protein Target Based on a Very Large Set of Pockets and Drug-like
Ligands from the Protein Data Bank},
journal = {J. Chem. Inf. Model.},
volume = {50},
number = {11},
pages = {2029--2040},
year = {2010},
url = {https://doi.org/10.1021/ci100312t},
doi = {10.1021/CI100312T},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/SheridanMHCG10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/TanBB10,
author = {Lu Tan and
Jos{\'{e}} Batista and
J{\"{u}}rgen Bajorath},
title = {Rationalization of the Performance and Target Dependence of Similarity
Searching Incorporating Protein-Ligand Interaction Information},
journal = {J. Chem. Inf. Model.},
volume = {50},
number = {6},
pages = {1042--1052},
year = {2010},
url = {https://doi.org/10.1021/ci1001197},
doi = {10.1021/CI1001197},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/TanBB10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jib/LeeDH10,
author = {Hang{-}mao Lee and
Karl J. Dietz and
Ralf Hofest{\"{a}}dt},
title = {Prediction of thioredoxin and glutaredoxin target proteins by identifying
reversibly oxidized cysteinyl residues},
journal = {J. Integr. Bioinform.},
volume = {7},
number = {3},
year = {2010},
url = {https://doi.org/10.2390/biecoll-jib-2010-130},
doi = {10.2390/BIECOLL-JIB-2010-130},
timestamp = {Tue, 14 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jib/LeeDH10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/PapamichailP10,
author = {Dimitris P. Papamichail and
Georgios Papamichail},
title = {Incorporating miRNA target sites in protein-coding {RNA}},
booktitle = {2010 {IEEE} International Conference on Bioinformatics and Biomedicine
Workshops, {BIBMW} 2010, Hong Kong, December 18, 2010},
pages = {380--385},
publisher = {{IEEE}},
year = {2010},
url = {https://doi.org/10.1109/BIBMW.2010.5703832},
doi = {10.1109/BIBMW.2010.5703832},
timestamp = {Wed, 24 Nov 2021 15:06:06 +0100},
biburl = {https://dblp.org/rec/conf/bibm/PapamichailP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@inproceedings{DBLP:conf/bibm/ParkLK10,
author = {Byeolna Park and
Yoon Kyeong Lee and
Hak Yong Kim},
title = {Transcriptional regulation of drug target proteins from cancer related
disease network},
booktitle = {2010 {IEEE} International Conference on Bioinformatics and Biomedicine
Workshops, {BIBMW} 2010, Hong Kong, December 18, 2010},
pages = {843--844},
publisher = {{IEEE}},
year = {2010},
url = {https://doi.org/10.1109/BIBMW.2010.5703937},
doi = {10.1109/BIBMW.2010.5703937},
timestamp = {Wed, 24 Nov 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/ParkLK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@inproceedings{DBLP:conf/jbi/MorillaMR10,
author = {Ian Morilla and
Miguel Angel Medina and
Juan A. G. Ranea},
editor = {Ana T. Freitas and
Arcadi Navarro},
title = {Novel Angiogenic Functional Targets Predicted through "Dark Matter"
Assessment in Protein Networks},
booktitle = {Bioinformatics for Personalized Medicine - 10th Spanish Symposium,
{JBI} 2010, Torremolinos, Spain, October 27-29, 2010. Revised Selected
Papers},
series = {Lecture Notes in Computer Science},
volume = {6620},
pages = {89--93},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-28062-7\_10},
doi = {10.1007/978-3-642-28062-7\_10},
timestamp = {Sun, 02 Jun 2019 21:12:35 +0200},
biburl = {https://dblp.org/rec/conf/jbi/MorillaMR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BakheetD09,
author = {Tala Bakheet and
Andrew J. Doig},
title = {Properties and identification of human protein drug targets},
journal = {Bioinform.},
volume = {25},
number = {4},
pages = {451--457},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp002},
doi = {10.1093/BIOINFORMATICS/BTP002},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BakheetD09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PivaGNP09,
author = {Francesco Piva and
Matteo Giulietti and
Linda Nocchi and
Giovanni Principato},
title = {SpliceAid: a database of experimental {RNA} target motifs bound by
splicing proteins in humans},
journal = {Bioinform.},
volume = {25},
number = {9},
pages = {1211--1213},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp124},
doi = {10.1093/BIOINFORMATICS/BTP124},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PivaGNP09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MaragkakisAPRDGGKKSSVKSTH09,
author = {Manolis Maragkakis and
Panagiotis Alexiou and
Giorgos L. Papadopoulos and
Martin Reczko and
Theodore Dalamagas and
Giorgos Giannopoulos and
George I. Goumas and
Evangelos Koukis and
Kornilios Kourtis and
Victor A. Simossis and
Praveen Sethupathy and
Thanasis Vergoulis and
Nectarios Koziris and
Timos K. Sellis and
Panayotis Tsanakas and
Artemis G. Hatzigeorgiou},
title = {Accurate microRNA target prediction correlates with protein repression
levels},
journal = {{BMC} Bioinform.},
volume = {10},
pages = {295},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-295},
doi = {10.1186/1471-2105-10-295},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MaragkakisAPRDGGKKSSVKSTH09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YeniterziS09,
author = {S{\"{u}}veyda Yeniterzi and
Osman Ugur Sezerman},
title = {EnzyMiner: automatic identification of protein level mutations and
their impact on target enzymes from PubMed abstracts},
journal = {{BMC} Bioinform.},
volume = {10},
number = {{S-8}},
pages = {2},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-S8-S2},
doi = {10.1186/1471-2105-10-S8-S2},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/YeniterziS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/NovakWK09,
author = {William Novak and
Hongming Wang and
Goran Krilov},
title = {Role of protein flexibility in the design of Bcl-X\({}_{\mbox{L}}\)
targeting agents: insight from molecular dynamics},
journal = {J. Comput. Aided Mol. Des.},
volume = {23},
number = {1},
pages = {49--61},
year = {2009},
url = {https://doi.org/10.1007/s10822-008-9237-0},
doi = {10.1007/S10822-008-9237-0},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/NovakWK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/YennamalliSKMYK09,
author = {Ragothaman Yennamalli and
Naidu Subbarao and
Thorsten Kampmann and
Ross P. McGeary and
Paul R. Young and
Bostjan Kobe},
title = {Identification of novel target sites and an inhibitor of the dengue
virus {E} protein},
journal = {J. Comput. Aided Mol. Des.},
volume = {23},
number = {6},
pages = {333--341},
year = {2009},
url = {https://doi.org/10.1007/s10822-009-9263-6},
doi = {10.1007/S10822-009-9263-6},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcamd/YennamalliSKMYK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/CaseyPS09,
author = {Fergal P. Casey and
Emilie Pihan and
Denis C. Shields},
title = {Discovery of Small Molecule Inhibitors of Protein-Protein Interactions
Using Combined Ligand and Target Score Normalization},
journal = {J. Chem. Inf. Model.},
volume = {49},
number = {12},
pages = {2708--2717},
year = {2009},
url = {https://doi.org/10.1021/ci900294x},
doi = {10.1021/CI900294X},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/CaseyPS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cocoon/SramekFVW09,
author = {Rastislav Sr{\'{a}}mek and
Bernd Fischer and
Elias Vicari and
Peter Widmayer},
editor = {Hung Q. Ngo},
title = {Optimal Transitions for Targeted Protein Quantification: Best Conditioned
Submatrix Selection},
booktitle = {Computing and Combinatorics, 15th Annual International Conference,
{COCOON} 2009, Niagara Falls, NY, USA, July 13-15, 2009, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5609},
pages = {287--296},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-02882-3\_29},
doi = {10.1007/978-3-642-02882-3\_29},
timestamp = {Tue, 14 May 2019 10:00:35 +0200},
biburl = {https://dblp.org/rec/conf/cocoon/SramekFVW09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AngaricaPVCC08,
author = {Vladimir Espinosa Angarica and
Abel Gonz{\'{a}}lez P{\'{e}}rez and
Ana Tereza Ribeiro de Vasconcelos and
Julio Collado{-}Vides and
Bruno Contreras{-}Moreira},
title = {Prediction of {TF} target sites based on atomistic models of protein-DNA
complexes},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-436},
doi = {10.1186/1471-2105-9-436},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AngaricaPVCC08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GaoLZLKLZCWJ08,
author = {Zhenting Gao and
Honglin Li and
Hailei Zhang and
Xiaofeng Liu and
Ling Kang and
Xiaomin Luo and
Weiliang Zhu and
Kaixian Chen and
Xicheng Wang and
Hualiang Jiang},
title = {{PDTD:} a web-accessible protein database for drug target identification},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-104},
doi = {10.1186/1471-2105-9-104},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/GaoLZLKLZCWJ08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MizunoKHOS08,
author = {Yumi Mizuno and
Igor Kurochkin and
Marlis Herberth and
Yasushi Okazaki and
Christian Sch{\"{o}}nbach},
title = {Predicted mouse peroxisome-targeted proteins and their actual subcellular
locations},
journal = {{BMC} Bioinform.},
volume = {9},
number = {{S-12}},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-S12-S16},
doi = {10.1186/1471-2105-9-S12-S16},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MizunoKHOS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/ChuC08,
author = {Liang{-}Hui Chu and
Bor{-}Sen Chen},
title = {Construction of a cancer-perturbed protein-protein interaction network
for discovery of apoptosis drug targets},
journal = {{BMC} Syst. Biol.},
volume = {2},
pages = {56},
year = {2008},
url = {https://doi.org/10.1186/1752-0509-2-56},
doi = {10.1186/1752-0509-2-56},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/ChuC08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijcbdd/HyunJJJH08,
author = {Bo{-}ra Hyun and
Hwiesung Jung and
Woo{-}Hyuk Jang and
Suk Hoon Jung and
Dong{-}Soo Han},
title = {Weighted feature value based Drug Target Protein prediction},
journal = {Int. J. Comput. Biol. Drug Des.},
volume = {1},
number = {4},
pages = {422--433},
year = {2008},
url = {https://doi.org/10.1504/IJCBDD.2008.022211},
doi = {10.1504/IJCBDD.2008.022211},
timestamp = {Sat, 25 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijcbdd/HyunJJJH08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/isb/WenFW08,
author = {Jiayu Wen and
Tancred Frickey and
Georg F. Weiller},
title = {Computational Prediction of Candidate miRNAs and their Targets from
Medicago truncatula Non-Protein-Coding Transcripts},
journal = {Silico Biol.},
volume = {8},
number = {3-4},
pages = {291--306},
year = {2008},
url = {http://content.iospress.com/articles/in-silico-biology/isb00359},
timestamp = {Thu, 20 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/isb/WenFW08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/KellenbergerFR08,
author = {Esther Kellenberger and
Nicolas Foata and
Didier Rognan},
title = {Ranking Targets in Structure-Based Virtual Screening of Three-Dimensional
Protein Libraries: Methods and Problems},
journal = {J. Chem. Inf. Model.},
volume = {48},
number = {5},
pages = {1014--1025},
year = {2008},
url = {https://doi.org/10.1021/ci800023x},
doi = {10.1021/CI800023X},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/KellenbergerFR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/HanK08,
author = {Sangjo Han and
Dongsup Kim},
title = {Inference of Protein Complex Activities from Chemical-Genetic Profile
and Its Applications: Predicting Drug-Target Pathways},
journal = {PLoS Comput. Biol.},
volume = {4},
number = {8},
year = {2008},
url = {https://doi.org/10.1371/journal.pcbi.1000162},
doi = {10.1371/JOURNAL.PCBI.1000162},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/HanK08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biocomp/LinXCS08,
author = {Shih{-}Fang Lin and
Ke{-}Ting Xiao and
Chung{-}Cheng Chiu and
Von{-}Wun Soo},
editor = {Hamid R. Arabnia and
Mary Qu Yang and
Jack Y. Yang},
title = {Classifying Proteins Related to Adverse Drug Reactions from Drug Targets
Using Support Vector Machines},
booktitle = {International Conference on Bioinformatics {\&} Computational
Biology, {BIOCOMP} 2008, July 14-17, 2008, Las Vegas Nevada, USA,
2 Volumes},
pages = {753--759},
publisher = {{CSREA} Press},
year = {2008},
timestamp = {Fri, 06 Feb 2009 11:52:50 +0100},
biburl = {https://dblp.org/rec/conf/biocomp/LinXCS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/PanWK08,
author = {Wei Pan and
Peng Wei and
Arkady B. Khodursky},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {A Parametric Joint Model of DNA-Protein Binding, Gene Expression and
{DNA} Sequence Data to Detect Target Genes of a Transcription Factor},
booktitle = {Biocomputing 2008, Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, 4-8 January 2008},
pages = {465--476},
publisher = {World Scientific},
year = {2008},
url = {http://psb.stanford.edu/psb-online/proceedings/psb08/pan.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/PanWK08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@inproceedings{DBLP:conf/wabi/LingnerM08,
author = {Thomas Lingner and
Peter Meinicke},
editor = {Keith A. Crandall and
Jens Lagergren},
title = {Fast Target Set Reduction for Large-Scale Protein Function Prediction:
{A} Multi-class Multi-label Machine Learning Approach},
booktitle = {Algorithms in Bioinformatics, 8th International Workshop, {WABI} 2008,
Karlsruhe, Germany, September 15-19, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5251},
pages = {198--209},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-87361-7\_17},
doi = {10.1007/978-3-540-87361-7\_17},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/LingnerM08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@article{DBLP:journals/bioinformatics/BhardwajSZCL07,
author = {Nitin Bhardwaj and
Robert V. Stahelin and
Guijun Zhao and
Wonhwa Cho and
Hui Lu},
title = {MeTaDoR: a comprehensive resource for membrane targeting domains and
their host proteins},
journal = {Bioinform.},
volume = {23},
number = {22},
pages = {3110--3112},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm395},
doi = {10.1093/BIOINFORMATICS/BTM395},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BhardwajSZCL07.bib},
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@article{DBLP:journals/bmcbi/HanzlikKTDF07,
author = {Robert P. Hanzlik and
Yakov M. Koen and
Bhargav Theertham and
Yinghua Dong and
Jianwen Fang},
title = {The reactive metabolite target protein database {(TPDB)} - a web-accessible
resource},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-95},
doi = {10.1186/1471-2105-8-95},
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biburl = {https://dblp.org/rec/journals/bmcbi/HanzlikKTDF07.bib},
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@article{DBLP:journals/bmcsb/FongPT07,
author = {Siew Fong and
Fiona E. M. Paulin and
Alastair Thompson},
title = {Computational identification of tumour suppressor protein p53 target
genes},
journal = {{BMC} Syst. Biol.},
volume = {1},
number = {{S-1}},
pages = {P8},
year = {2007},
url = {https://doi.org/10.1186/1752-0509-1-S1-P8},
doi = {10.1186/1752-0509-1-S1-P8},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/FongPT07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@article{DBLP:journals/jbcb/IvanovGMMLA07,
author = {Alexis S. Ivanov and
Oksana V. Gnedenko and
Andrey A. Molnar and
Yury V. Mezentsev and
Andrey Lisitsa and
Alexander I. Archakov},
title = {Protein-protein Interactions as New Targets for Drug Design: Virtual
and Experimental Approaches},
journal = {J. Bioinform. Comput. Biol.},
volume = {5},
number = {2b},
pages = {579--592},
year = {2007},
url = {https://doi.org/10.1142/S0219720007002825},
doi = {10.1142/S0219720007002825},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/IvanovGMMLA07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@inproceedings{DBLP:conf/ismb/DawelbaitWZPGHS07,
author = {Gihan Dawelbait and
Christof Winter and
Yanju Zhang and
Christian Pilarsky and
Robert Gr{\"{u}}tzmann and
J{\"{o}}rg{-}Christian Heinrich and
Michael Schroeder},
title = {Structural templates predict novel protein interactions and targets
from pancreas tumour gene expression data},
booktitle = {Proceedings 15th International Conference on Intelligent Systems for
Molecular Biology {(ISMB)} {\&} 6th European Conference on Computational
Biology (ECCB), Vienna, Austria, July 21-25, 2007},
pages = {115--124},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm188},
doi = {10.1093/BIOINFORMATICS/BTM188},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/DawelbaitWZPGHS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@article{DBLP:journals/bioinformatics/HoglundDBAK06,
author = {Annette H{\"{o}}glund and
Pierre D{\"{o}}nnes and
Torsten Blum and
Hans{-}Werner Adolph and
Oliver Kohlbacher},
title = {MultiLoc: prediction of protein subcellular localization using N-terminal
targeting sequences, sequence motifs and amino acid composition},
journal = {Bioinform.},
volume = {22},
number = {10},
pages = {1158--1165},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl002},
doi = {10.1093/BIOINFORMATICS/BTL002},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HoglundDBAK06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@article{DBLP:journals/ijmi/PyysaloGPBJS06,
author = {Sampo Pyysalo and
Filip Ginter and
Tapio Pahikkala and
Jorma Boberg and
Jouni J{\"{a}}rvinen and
Tapio Salakoski},
title = {Evaluation of two dependency parsers on biomedical corpus targeted
at protein-protein interactions},
journal = {Int. J. Medical Informatics},
volume = {75},
number = {6},
pages = {430--442},
year = {2006},
url = {https://doi.org/10.1016/j.ijmedinf.2005.06.009},
doi = {10.1016/J.IJMEDINF.2005.06.009},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijmi/PyysaloGPBJS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@article{DBLP:journals/jbcb/LiJC06,
author = {Yvonne Y. Li and
Steven J. M. Jones and
Artem Cherkasov},
title = {Selective Targeting of Indel-inferred Differences in Spatial Structures
of Homologous Proteins},
journal = {J. Bioinform. Comput. Biol.},
volume = {4},
number = {2},
pages = {403--414},
year = {2006},
url = {https://doi.org/10.1142/S0219720006001898},
doi = {10.1142/S0219720006001898},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/LiJC06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@article{DBLP:journals/jcamd/Kennewell0DL06,
author = {Elizabeth A. Kennewell and
Peter Willett and
Pierre Ducrot and
Claude Luttmann},
title = {Identification of target-specific bioisosteric fragments from ligand-protein
crystallographic data},
journal = {J. Comput. Aided Mol. Des.},
volume = {20},
number = {6},
pages = {385--394},
year = {2006},
url = {https://doi.org/10.1007/s10822-006-9072-0},
doi = {10.1007/S10822-006-9072-0},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Kennewell0DL06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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@article{DBLP:journals/jcamd/SinghCFM06,
author = {Nidhi Singh and
Gw{\'{e}}na{\"{e}}l Chev{\'{e}} and
David M. Ferguson and
Christopher R. McCurdy},
title = {A combined ligand-based and target-based drug design approach for
G-protein coupled receptors: application to salvinorin A, a selective
kappa opioid receptor agonist},
journal = {J. Comput. Aided Mol. Des.},
volume = {20},
number = {7-8},
pages = {471--493},
year = {2006},
url = {https://doi.org/10.1007/s10822-006-9067-x},
doi = {10.1007/S10822-006-9067-X},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/SinghCFM06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/FukunishiKN06,
author = {Yoshifumi Fukunishi and
Satoru Kubota and
Haruki Nakamura},
title = {Noise Reduction Method for Molecular Interaction Energy: Application
to in Silico Drug Screening and in Silico Target Protein Screening},
journal = {J. Chem. Inf. Model.},
volume = {46},
number = {5},
pages = {2071--2084},
year = {2006},
url = {https://doi.org/10.1021/ci060152z},
doi = {10.1021/CI060152Z},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/FukunishiKN06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SinghCAM06,
author = {Nidhi Singh and
Gw{\'{e}}na{\"{e}}l Chev{\'{e}} and
Mitchell A. Avery and
Christopher R. McCurdy},
title = {Comparative Protein Modeling of 1-Deoxy-D-xylulose-5-phosphate Reductoisomerase
Enzyme from \emph{Plasmodium }\emph{f}\emph{alciparum}: {A} Potential
Target for Antimalarial Drug Discovery},
journal = {J. Chem. Inf. Model.},
volume = {46},
number = {3},
pages = {1360--1370},
year = {2006},
url = {https://doi.org/10.1021/ci050523w},
doi = {10.1021/CI050523W},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/SinghCAM06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/RanjanSVYR06,
author = {Sarita Ranjan and
Jayashree Seshadri and
Vaibhav Vindal and
Sailu Yellaboina and
Akash Ranjan},
title = {iCR: a web tool to identify conserved targets of a regulatory protein
across the multiple related prokaryotic species},
journal = {Nucleic Acids Res.},
volume = {34},
number = {Web-Server-Issue},
pages = {584--587},
year = {2006},
url = {https://doi.org/10.1093/nar/gkl202},
doi = {10.1093/NAR/GKL202},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/RanjanSVYR06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/RuthsTNR06,
author = {Derek A. Ruths and
Jen{-}Te Tseng and
Luay Nakhleh and
Prahlad T. Ram},
editor = {Trey Ideker and
Vineet Bafna},
title = {De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction,
Targeted Therapy and Protein Microarray Analysis},
booktitle = {Systems Biology and Computational Proteomics, Joint {RECOMB} 2006
Satellite Workshops on Systems Biology and on Computational Proteomics,
San Diego, CA, USA, December 1-3, 2006, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {4532},
pages = {108--118},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/978-3-540-73060-6\_8},
doi = {10.1007/978-3-540-73060-6\_8},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/RuthsTNR06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sac/ChenPSW06,
author = {Jake Yue Chen and
Sarah L. Pinkerton and
Changyu Shen and
Mu Wang},
editor = {Hisham Haddad},
title = {An integrated computational proteomics method to extract protein targets
for Fanconi Anemia studies},
booktitle = {Proceedings of the 2006 {ACM} Symposium on Applied Computing (SAC),
Dijon, France, April 23-27, 2006},
pages = {173--179},
publisher = {{ACM}},
year = {2006},
url = {https://doi.org/10.1145/1141277.1141316},
doi = {10.1145/1141277.1141316},
timestamp = {Wed, 19 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/sac/ChenPSW06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sc/WalkerRB06,
author = {Ross C. Walker and
Srivatsan Raman and
David Baker},
title = {Poster reception - High resolution, high throughput protein structure
prediction using {IBM} Blue Gene supercomputers: predicting {CASP}
targets in record time},
booktitle = {Proceedings of the {ACM/IEEE} {SC2006} Conference on High Performance
Networking and Computing, November 11-17, 2006, Tampa, FL, {USA}},
pages = {165},
publisher = {{ACM} Press},
year = {2006},
url = {https://doi.org/10.1145/1188455.1188626},
doi = {10.1145/1188455.1188626},
timestamp = {Wed, 16 Oct 2019 14:14:57 +0200},
biburl = {https://dblp.org/rec/conf/sc/WalkerRB06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CameronHR05,
author = {J. M. Cameron and
T. Hurd and
B. H. Robinson},
title = {Computational identification of human mitochondrial proteins based
on homology to yeast mitochondrially targeted proteins},
journal = {Bioinform.},
volume = {21},
number = {9},
pages = {1825--1830},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti280},
doi = {10.1093/BIOINFORMATICS/BTI280},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CameronHR05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GudaS05,
author = {Chittibabu Guda and
Shankar Subramaniam},
title = {{TARGET:} a new method for predicting protein subcellular localization
in eukaryotes},
journal = {Bioinform.},
volume = {21},
number = {21},
pages = {3963--3969},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti650},
doi = {10.1093/BIOINFORMATICS/BTI650},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GudaS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/TodorovBA05,
author = {Nikolay P. Todorov and
Christoph L. Buenemann and
Ian L. Alberts},
title = {Combinatorial Ligand Design Targeted at Protein Families},
journal = {J. Chem. Inf. Model.},
volume = {45},
number = {2},
pages = {314--320},
year = {2005},
url = {https://doi.org/10.1021/ci049692r},
doi = {10.1021/CI049692R},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/TodorovBA05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/HoglundDBAK05,
author = {Annette H{\"{o}}glund and
Pierre D{\"{o}}nnes and
Torsten Blum and
Hans{-}Werner Adolph and
Oliver Kohlbacher},
editor = {Andrew E. Torda and
Stefan Kurtz and
Matthias Rarey},
title = {Using N-terminal targeting sequences, amino acid composition, and
sequence motifs for predicting protein subcellular localizations},
booktitle = {Proceedings of the German Conference on Bioinformatics {(GCB} 2005),
Hamburg, Germany, October 5-7, 2005},
series = {{LNI}},
volume = {{P-71}},
pages = {45--59},
publisher = {{GI}},
year = {2005},
url = {https://dl.gi.de/handle/20.500.12116/24939},
timestamp = {Tue, 04 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gcb/HoglundDBAK05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BaurinABDDDFFRSH04,
author = {Nicolas Baurin and
Fareed Aboul{-}Ela and
Xavier Barril and
Ben Davis and
Martin Drysdale and
Brian Dymock and
Harry Finch and
Christophe Fromont and
Christine M. Richardson and
Heather Simmonite and
Roderick E. Hubbard},
title = {Design and Characterization of Libraries of Molecular Fragments for
Use in {NMR} Screening against Protein Targets},
journal = {J. Chem. Inf. Model.},
volume = {44},
number = {6},
pages = {2157--2166},
year = {2004},
url = {https://doi.org/10.1021/ci049806z},
doi = {10.1021/CI049806Z},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/BaurinABDDDFFRSH04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/PyysaloGPBJSK04,
author = {Sampo Pyysalo and
Filip Ginter and
Tapio Pahikkala and
Jorma Boberg and
Jouni J{\"{a}}rvinen and
Tapio Salakoski and
Jeppe Koivula},
editor = {Nigel Collier and
Patrick Ruch and
Adeline Nazarenko},
title = {Analysis of Link Grammar on Biomedical Dependency Corpus Targeted
at Protein-Protein Interactions},
booktitle = {Proceedings of the International Joint Workshop on Natural Language
Processing in Biomedicine and its Applications, NLPBA/BioNLP 2004,
Geneva, Switzerland, August 28-29, 2004},
year = {2004},
url = {https://aclanthology.org/W04-1203/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/PyysaloGPBJSK04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dmkdttt/DengHPT04,
author = {Hai Deng and
Robert W. Harrison and
Yi Pan and
Phang C. Tai},
editor = {Belur V. Dasarathy},
title = {Alternative target functions for protein structure prediction with
neural networks},
booktitle = {Data Mining and Knowledge Discovery: Theory, Tools, and Technology
VI, Orlando, FL, USA, April 12, 2004},
series = {{SPIE} Proceedings},
volume = {5433},
pages = {100--107},
publisher = {{SPIE}},
year = {2004},
url = {https://doi.org/10.1117/12.542253},
doi = {10.1117/12.542253},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/dmkdttt/DengHPT04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MohanA03,
author = {K. V. Krishna Mohan and
C. D. Atreya},
title = {Novel organelle-targeting signals in viral proteins},
journal = {Bioinform.},
volume = {19},
number = {1},
pages = {10--13},
year = {2003},
url = {https://doi.org/10.1093/bioinformatics/19.1.10},
doi = {10.1093/BIOINFORMATICS/19.1.10},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MohanA03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcamd/Pirard03,
author = {Bernard Pirard},
title = {Peroxisome Proliferator-Activated Receptors target family landscape:
{A} chemometrical approach to ligand selectivity based on protein
binding site analysis},
journal = {J. Comput. Aided Mol. Des.},
volume = {17},
number = {11},
pages = {785--796},
year = {2003},
url = {https://doi.org/10.1023/B:JCAM.0000017498.74580.3d},
doi = {10.1023/B:JCAM.0000017498.74580.3D},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcamd/Pirard03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/BalakinLSTIS03,
author = {Konstantin V. Balakin and
Stanley A. Lang and
Andrey V. Skorenko and
Sergey E. Tkachenko and
Andrey A. Ivashchenko and
Nikolay P. Savchuk},
title = {Structure-Based versus Property-Based Approaches in the Design of
G-Protein-Coupled Receptor-Targeted Libraries},
journal = {J. Chem. Inf. Comput. Sci.},
volume = {43},
number = {5},
pages = {1553--1562},
year = {2003},
url = {https://doi.org/10.1021/ci034114g},
doi = {10.1021/CI034114G},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/BalakinLSTIS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/SchuffenhauerFAJ03,
author = {Ansgar Schuffenhauer and
Philipp Floersheim and
Pierre Acklin and
Edgar Jacoby},
title = {Similarity Metrics for Ligands Reflecting the Similarity of the Target
Proteins},
journal = {J. Chem. Inf. Comput. Sci.},
volume = {43},
number = {2},
pages = {391--405},
year = {2003},
url = {https://doi.org/10.1021/ci025569t},
doi = {10.1021/CI025569T},
timestamp = {Thu, 14 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcisd/SchuffenhauerFAJ03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SardielloLCAC03,
author = {Marco Sardiello and
Flavio Licciulli and
Domenico Catalano and
Marcella Attimonelli and
Corrado Caggese},
title = {MitoDrome: a database of Drosophila melanogaster nuclear genes encoding
proteins targeted to the mitochondrion},
journal = {Nucleic Acids Res.},
volume = {31},
number = {1},
pages = {322--324},
year = {2003},
url = {https://doi.org/10.1093/nar/gkg123},
doi = {10.1093/NAR/GKG123},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SardielloLCAC03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PortugalyKL02,
author = {Elon Portugaly and
Ilona Kifer and
Michal Linial},
title = {Selecting targets for structural determination by navigating in a
graph of protein families},
journal = {Bioinform.},
volume = {18},
number = {7},
pages = {899--907},
year = {2002},
url = {https://doi.org/10.1093/bioinformatics/18.7.899},
doi = {10.1093/BIOINFORMATICS/18.7.899},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PortugalyKL02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/ManallackPGMLFW02,
author = {David T. Manallack and
Will R. Pitt and
Emanuela Gancia and
John G. Montana and
David J. Livingstone and
Martyn G. Ford and
David C. Whitley},
title = {Selecting Screening Candidates for Kinase and {G} Protein-Coupled
Receptor Targets Using Neural Networks},
journal = {J. Chem. Inf. Comput. Sci.},
volume = {42},
number = {5},
pages = {1256--1262},
year = {2002},
url = {https://doi.org/10.1021/ci020267c},
doi = {10.1021/CI020267C},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/ManallackPGMLFW02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HodgesCHOOMDBG03,
author = {Peter E. Hodges and
Pauline M. Carrico and
Jennifer D. Hogan and
Kathy E. O'Neill and
J. J. Owen and
Mary E. Mangan and
Brian P. Davis and
Joan E. Brooks and
James I. Garrels},
title = {Annotating the human proteome: the Human Proteome Survey Database
(HumanPSDTM) and an in-depth target database for {G} protein-coupled
receptors {(GPCR-PDTM)} from Incyte Genomics},
journal = {Nucleic Acids Res.},
volume = {30},
number = {1},
pages = {137--141},
year = {2002},
url = {https://doi.org/10.1093/nar/30.1.137},
doi = {10.1093/NAR/30.1.137},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HodgesCHOOMDBG03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/Patterson02,
author = {Scott Patterson},
title = {Selecting targets for therapeutic validation through differential
protein expression using chromatography-mass spectrometry},
booktitle = {Proceedings of the European Conference on Computational Biology {(ECCB}
2002), October 6-9, 2002, Saarbr{\"{u}}cken, Germany},
pages = {181},
year = {2002},
timestamp = {Thu, 23 Jun 2016 15:53:27 +0200},
biburl = {https://dblp.org/rec/conf/eccb/Patterson02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sac/Grigoriev01,
author = {Igor V. Grigoriev},
editor = {Gary B. Lamont},
title = {Computational structural genomics: identifying protein targets for
structural studies},
booktitle = {Proceedings of the 2001 {ACM} Symposium on Applied Computing (SAC),
March 11-14, 2001, Las Vegas, NV, {USA}},
pages = {41--45},
publisher = {{ACM}},
year = {2001},
url = {https://doi.org/10.1145/372202.372269},
doi = {10.1145/372202.372269},
timestamp = {Wed, 25 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/sac/Grigoriev01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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author = {T. Wei and
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biburl = {https://dblp.org/rec/journals/bioinformatics/WeiO99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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author = {I. V. Boni and
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biburl = {https://dblp.org/rec/journals/nar/BoniIMT91.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
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