• case-insensitive prefix search: default
  e.g., sig matches "SIGIR" as well as "signal"
• exact word search: append dollar sign ($) to word
  e.g., graph$ matches "graph", but not "graphics"
• boolean and: separate words by space
  e.g., codd model
• boolean or: connect words by pipe symbol (|)
  e.g., graph|network

Update May 7, 2017: Please note that we had to disable the phrase search operator (.) and the boolean not operator (-) due to technical problems. For the time being, phrase search queries will yield regular prefix search result, and search terms preceded by a minus will be interpreted as regular (positive) search terms.

found 100 matches

• 2024
• 
  Anna Carbery, Martin Buttenschoen, Rachael Skyner, Frank von Delft, Charlotte M. Deane:
  Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures. J. Cheminformatics 16(1): 32 (2024)
• 
  Jiaming Gao, Haoquan Liu, Chen Zhuo, Chengwei Zeng, Yunjie Zhao:
  Predicting Small Molecule Binding Nucleotides in RNA Structures Using RNA Surface Topography. J. Chem. Inf. Model. 64(18): 6979-6992 (2024)
• 
  Rong Han, Xiaohong Liu, Tong Pan, Jing Xu, Xiaoyu Wang, Wuyang Lan, Zhenyu Li, Zixuan Wang, Jiangning Song, Guangyu Wang, Ting Chen:
  CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction. CoRR abs/2409.03773 (2024)
• 2023
• 
  Yidong Song, Qianmu Yuan, Huiying Zhao, Yuedong Yang:
  Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures. Briefings Bioinform. 24(6) (2023)
• 
  Yanpeng Zhao, Jingjing Wang, Fubin Chang, Weikang Gong, Yang Liu, Chunhua Li:
  Identification of metal ion-binding sites in RNA structures using deep learning method. Briefings Bioinform. 24(2) (2023)
• 
  Vid Ravnik, Marko Jukic, Urban Bren:
  Identifying Metal Binding Sites in Proteins Using Homologous Structures, the MADE Approach. J. Chem. Inf. Model. 63(16): 5204-5219 (2023)
• 2022
• 
  Vinícius de Almeida Paiva, Murillo Ventura Mendonça, Sabrina de Azevedo Silveira, David B. Ascher, Douglas E. V. Pires, Sandro C. Izidoro:
  GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms. Briefings Bioinform. 23(5) (2022)
• 
  Swati Adhikari, Parthajit Roy:
  A geometry based approach to compare five metal binding sites on biomolecular structures. Int. J. Comput. Biol. Drug Des. 15(1): 1-29 (2022)
• 
  Janez Konc, Dusanka Janezic:
  ProBiS-Fold Approach for Annotation of Human Structures from the AlphaFold Database with No Corresponding Structure in the PDB to Discover New Druggable Binding Sites. J. Chem. Inf. Model. 62(22): 5821-5829 (2022)
• 
  Vincenzo Laveglia, Andrea Giachetti, Davide Sala, Claudia Andreini, Antonio Rosato:
  Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network. J. Chem. Inf. Model. 62(12): 2951-2960 (2022)
• 
  Huiyan Lu, Yuji Komukai, Koto Usami, Yan Guo, Xinyue Qiao, Michiyoshi Nukaga, Tyuji Hoshino:
  Computational and Crystallographic Analysis of Binding Structures of Inhibitory Compounds for HIV-1 RNase H Activity. J. Chem. Inf. Model. 62(24): 6762-6774 (2022)
• 
  Jinze Zhang, Hao Li, Xuejun Zhao, Qilong Wu, Sheng-You Huang:
  Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement. J. Chem. Inf. Model. 62(22): 5806-5820 (2022)
• 
  David Jakubec, Petr Skoda, Radoslav Krivák, Marian Novotny, David Hoksza:
  PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures. Nucleic Acids Res. 50(W1): 593-597 (2022)
• 2021
• 
  Wajid Arshad Abbasi, Syed Ali Abbas, Saiqa Andleeb:
  PANDA: Predicting the change in proteins binding affinity upon mutations by finding a signal in primary structures. J. Bioinform. Comput. Biol. 19(4): 2150015:1-2150015:19 (2021)
• 
  Hugo Guterres, Sang-Jun Park, Wei Jiang, Wonpil Im:
  Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures. J. Chem. Inf. Model. 61(1): 535-546 (2021)
• 2020
• 
  Rostislav K. Skitchenko, Dmitrii Usoltsev, Mayya Uspenskaya, Andrey V. Kajava, Albert Guskov:
  Census of halide-binding sites in protein structures. Bioinform. 36(10): 3064-3071 (2020)
• 
  Takashi Yoshidome, Mitsunori Ikeguchi, Masateru Ohta:
  Comprehensive 3D-RISM analysis of the hydration of small molecule binding sites in ligand-free protein structures. J. Comput. Chem. 41(28): 2406-2419 (2020)
• 
  Lucia Fusani, David S. Palmer, Don O. Somers, Ian D. Wall:
  Exploring Ligand Stability in Protein Crystal Structures Using Binding Pose Metadynamics. J. Chem. Inf. Model. 60(3): 1528-1539 (2020)
• 
  Tomohide Masuda, Matthew Ragoza, David Ryan Koes:
  Generating 3D Molecular Structures Conditional on a Receptor Binding Site with Deep Generative Models. CoRR abs/2010.14442 (2020)
• 2019
• 
  Zhe Wang, Xuwen Wang, Youyong Li, Tailong Lei, Ercheng Wang, Dan Li, Yu Kang, Feng Zhu, Tingjun Hou:
  farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods. Bioinform. 35(10): 1777-1779 (2019)
• 
  Mei Qian Yau, Abigail L. Emtage, Nathaniel J. Y. Chan, Stephen W. Doughty, Jason S. E. Loo:
  Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures. J. Comput. Aided Mol. Des. 33(5): 487-496 (2019)
• 
  Awatef Hattab, Zoubeida Dhaouadi, Alhadji Malloum, Jean Jules Fifen, Souad Lahmar, Nino Russo, Emilia Sicilia:
  Structures, binding energies, temperature effects, infrared spectroscopy of [Mg(NH3)n = 1-10]+ clusters from DFT and MP2 investigations. J. Comput. Chem. 40(18): 1707-1717 (2019)
• 
  François Bonnardel, Julien Mariethoz, Sebastian Salentin, Xavier Robin, Michael Schroeder, Serge Pérez, Frédérique Lisacek, Anne Imberty:
  UniLectin3D, a database of carbohydrate binding proteins with curated information on 3D structures and interacting ligands. Nucleic Acids Res. 47(Database-Issue): D1236-D1244 (2019)
• 2018
• 
  Damiano Piovesan, Silvio C. E. Tosatto:
  Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures. Bioinform. 34(1): 122-123 (2018)
• 
  Claas Strecker, Bernd Meyer:
  Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking. J. Chem. Inf. Model. 58(5): 1121-1131 (2018)
• 2017
• 
  Xia Lin, Michael Khoo, Jae-wook Ahn, Douglas Tudhope, Ceri Binding, Diane Massam, Hilary Jane Jones:
  Mapping metadata to DDC classification structures for searching and browsing. Int. J. Digit. Libr. 18(1): 25-39 (2017)
• 2016
• 
  Xihao Hu, Yang Wu, Zhi John Lu, Kevin Y. Yip:
  Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations. Briefings Bioinform. 17(6): 1032-1043 (2016)
• 
  Hoon Ryu, Yosang Jeong, Ji Hoon Kang, Kyunam Cho:
  Time-efficient simulations of tight-binding electronic structures with Intel Xeon Phi^TM many-core processors. Comput. Phys. Commun. 209: 79-87 (2016)
• 
  Li Rao, Bo Chi, Yanliang Ren, Yongjian Li, Xin Xu, Jian Wan:
  DOX: A new computational protocol for accurate prediction of the protein-ligand binding structures. J. Comput. Chem. 37(3): 336-344 (2016)
• 
  Joshua Meyers, Nathan Brown, Julian Blagg:
  Mapping the 3D structures of small molecule binding sites. J. Cheminformatics 8(1): 70:1-70:13 (2016)

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