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Publication search results
found 346 matches
- 2024
- Zi Liu, Chengxin Zhang, Qidi Zhang, Yang Zhang, Dong-Jun Yu:
TM-search: An Efficient and Effective Tool for Protein Structure Database Search. J. Chem. Inf. Model. 64(3): 1043-1049 (2024) - 2023
- Mingchen Li, Liqi Kang, Yi Xiong, Yu Guang Wang, Guisheng Fan, Pan Tan, Liang Hong:
SESNet: sequence-structure feature-integrated deep learning method for data-efficient protein engineering. J. Cheminformatics 15(1): 12 (2023) - Arup Mondal, G. V. T. Swapna, Maria M. Lopez, Laura Klang, Jingzhou Hao, Lichung Ma, Monica J. Roth, Gaetano T. Montelione, Alberto Perez:
Structure Determination of Challenging Protein-Peptide Complexes Combining NMR Chemical Shift Data and Molecular Dynamics Simulations. J. Chem. Inf. Model. 63(7): 2058-2072 (2023) - Zi Hao Liu, Oufan Zhang, João M. C. Teixeira, Jie Li, Teresa Head-Gordon, Julie D. Forman-Kay:
SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures. J. Open Source Softw. 8(86): 4861 (2023) - Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Henry Chao, Li Chen, Paul A. Craig, Gregg V. Crichlow, Kenneth Dalenberg, Jose M. Duarte, Shuchismita Dutta, Maryam Fayazi, Zukang Feng, Justin W. Flatt, Sai Ganesan, Sutapa Ghosh, David S. Goodsell, Rachel Kramer Green, Vladimir Guranovic, Jeremy Henry, Brian P. Hudson, Igor Khokhriakov, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Ezra Peisach, Irina Persikova, Dennis W. Piehl, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Brinda Vallat, Maria Voigt, Ben M. Webb, John D. Westbrook, Shamara Whetstone, Jasmine Young, Arthur O. Zalevsky, Christine Zardecki:
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning. Nucleic Acids Res. 51(D1): 488-508 (2023) - Laszlo Dobson, Levente I Szekeres, Csongor Gerdán, Tamás Langó, András Zeke, Gábor E. Tusnády:
TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures. Nucleic Acids Res. 51(D1): 517-522 (2023) - Shamima Rashid, Suresh Sundaram, Chee Keong Kwoh:
Empirical Study of Protein Feature Representation on Deep Belief Networks Trained With Small Data for Secondary Structure Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. 20(2): 955-966 (2023) - Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He:
An Approach to Developing Benchmark Datasets for Protein Secondary Structure Segmentation from Cryo-EM Density Maps. BCB 2023: 102:1-102:8 - Masanori Yamanaka:
Data mining of electronic structure of proteins and quantum evolution. IEEE Big Data 2023: 6314-6316 - Tim Kucera, Carlos G. Oliver, Dexiong Chen, Karsten M. Borgwardt:
ProteinShake: Building datasets and benchmarks for deep learning on protein structures. NeurIPS 2023 - Mingchen Li, Liqi Kang, Yi Xiong, Yu Guang Wang, Guisheng Fan, Pan Tan, Liang Hong:
SESNet: sequence-structure feature-integrated deep learning method for data-efficient protein engineering. CoRR abs/2301.00004 (2023) - Yufei Huang, Lirong Wu, Haitao Lin, Jiangbin Zheng, Ge Wang, Stan Z. Li:
Data-Efficient Protein 3D Geometric Pretraining via Refinement of Diffused Protein Structure Decoy. CoRR abs/2302.10888 (2023) - 2022
- Teerna Bhattacharyya, Soumya Nayak, Smit Goswami, Vasundhara Gadiyaram, Oommen K. Mathew, Ramanathan Sowdhamini:
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe. Database J. Biol. Databases Curation 2022(2022) (2022) - Aleksandra E. Badaczewska-Dawid, Javier Garcia-Pardo, Aleksander Kuriata, Jordi Pujols, Salvador Ventura, Sebastian Kmiecik:
A3D database: structure-based predictions of protein aggregation for the human proteome. Bioinform. 38(11): 3121-3123 (2022) - Sebastian Bittrich, Yana Rose, Joan Segura, Robert Lowe, John D. Westbrook, Jose M. Duarte, Stephen K. Burley:
RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB. Bioinform. 38(5): 1452-1454 (2022) - Nahuel Escobedo, Ronaldo Romario Tunque Cahui, Gastón Caruso, Emilio Garcia-Rios, Layla Hirsh, Alexander Miguel Monzon, Gustavo D. Parisi, Nicolas Palopoli:
CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure. Bioinform. 38(21): 4959-4961 (2022) - Emilia A. Lubecka, Adam Liwo:
A coarse-grained approach to NMR-data-assisted modeling of protein structures. J. Comput. Chem. 43(31): 2047-2059 (2022) - Mihaly Varadi, Stephen Anyango, Mandar S. Deshpande, Sreenath Nair, Cindy Natassia, Galabina Yordanova, David Yuan, Oana Stroe, Gemma Wood, Agata Laydon, Augustin Zídek, Tim Green, Kathryn Tunyasuvunakool, Stig Petersen, John Jumper, Ellen Clancy, Richard Green, Ankur Vora, Mira Lutfi, Michael Figurnov, Andrew Cowie, Nicole Hobbs, Pushmeet Kohli, Gerard J. Kleywegt, Ewan Birney, Demis Hassabis, Sameer Velankar:
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 50(D1): 439-444 (2022) - Mario Garza-Fabre, Julia Handl:
Protein Structure and Synthetic Multi-view Clustering Datasets. IEEE DataPort, 2022 - Sirui Liu, Jun Zhang, Haotian Chu, Min Wang, Boxin Xue, Ningxi Ni, Jialiang Yu, Yuhao Xie, Zhenyu Chen, Mengyun Chen, Yuan Liu, Piya Patra, Fan Xu, Jie Chen, Zidong Wang, Lijiang Yang, Fan Yu, Lei Chen, Yi Qin Gao:
PSP: Million-level Protein Sequence Dataset for Protein Structure Prediction. CoRR abs/2206.12240 (2022) - 2021
- Ivana Hutarová Vareková, Jan Hutar, Adam Midlik, Vladimír Horský, Eva Hladká, Radka Svobodová Vareková, Karel Berka:
2DProts: database of family-wide protein secondary structure diagrams. Bioinform. 37(23): 4599-4601 (2021) - Jan Niclas Wolf, Marcus Keßler, Jörg Ackermann, Ina Koch:
PTGL: extension to graph-based topologies of cryo-EM data for large protein structures. Bioinform. 37(7): 1032-1034 (2021) - Stephen K. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V. Crichlow, Cole H. Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M. Duarte, Shuchismita Dutta, Zukang Feng, Sai Ganesan, David S. Goodsell, Sutapa Ghosh, Rachel Kramer Green, Vladimir Guranovic, Dmytro Guzenko, Brian P. Hudson, Catherine L. Lawson, Yuhe Liang, Robert Lowe, Harry Namkoong, Ezra Peisach, Irina Persikova, Christopher Randle, Alexander S. Rose, Yana Rose, Andrej Sali, Joan Segura, Monica Sekharan, Chenghua Shao, Yi-Ping Tao, Maria Voigt, John D. Westbrook, Jasmine Young, Christine Zardecki, Marina Zhuravleva:
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. Nucleic Acids Res. 49(Database-Issue): D437-D451 (2021) - Ragul Gowthaman, Johnathan D. Guest, Rui Yin, Jared Adolf-Bryfogle, William R. Schief, Brian G. Pierce:
CoV3D: a database of high resolution coronavirus protein structures. Nucleic Acids Res. 49(Database-Issue): D282-D287 (2021) - Lisanna Paladin, Martina Bevilacqua, Sara Errigo, Damiano Piovesan, Ivan Micetic, Marco Necci, Alexander Miguel Monzon, Maria Laura Fabre, José Luis López, Juliet F. Nilsson, Javier Ríos, Pablo Lorenzano Menna, Maia Cabrera, Martin Gonzalez Buitron, Mariane Gonçalves Kulik, Sebastian Fernandez Alberti, María Silvina Fornasari, Gustavo D. Parisi, Antonio Lagares, Layla Hirsh, Miguel A. Andrade-Navarro, Andrey V. Kajava, Silvio C. E. Tosatto:
RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures. Nucleic Acids Res. 49(Database-Issue): D452-D457 (2021) - Bi Zhao, Akila Katuwawala, Christopher J. Oldfield, A. Keith Dunker, Eshel Faraggi, Jörg Gsponer, Andrzej Kloczkowski, Nawar Malhis, Milot Mirdita, Zoran Obradovic, Johannes Söding, Martin Steinegger, Yaoqi Zhou, Lukasz A. Kurgan:
DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Res. 49(Database-Issue): D298-D308 (2021) - Casey A. Cole, Nourhan S. Daigham, Gaohua Liu, Gaetano T. Montelione, Homayoun Valafar:
REDCRAFT: A computational platform using residual dipolar coupling NMR data for determining structures of perdeuterated proteins in solution. PLoS Comput. Biol. 17(2) (2021) - Michaela Areti Zervou, Effrosyni Doutsi, Panagiotis Tsakalides:
Visibility Graph Network of Multidimensional Time Series Data for Protein Structure Classification. EUSIPCO 2021: 1216-1220 - Taseef Rahman, Yuanqi Du, Liang Zhao, Amarda Shehu:
Dataset for Generative Adversarial Learning of Protein Tertiary Structures. Molecules, 2021. IEEE DataPort, 2021 - Alex Morehead, Chen Chen, Ada Sedova, Jianlin Cheng:
DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction. CoRR abs/2106.04362 (2021)
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