ZDOCK: An initial‐stage protein‐docking algorithm

Cited by (1,002)

Items 101–200 of 1,002

1. Building Macromolecular Assemblies by Information-driven Docking
   Ezgi Karaca, Adrien S. J. Melquiond, Sjoerd J. de Vries, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin · 2010 · Molecular & Cellular Proteomics
2. GalaxyRefineComplex: Refinement of protein-protein complex model structures driven by interface repacking
   Lim Heo, Hasup Lee, Chaok Seok · 2016 · Scientific Reports
3. An Expanded Benchmark for Antibody-Antigen Docking and Affinity Prediction Reveals Insights into Antibody Recognition Determinants
   Johnathan D. Guest, Thom Vreven, Jing Zhou, Iain H. Moal, Jeliazko R. Jeliazkov, Jeffrey J. Gray, Zhiping Weng, Brian G. Pierce · 2020 · Structure
4. Virtual Screening Techniques in Drug Discovery: Review and Recent Applications
   Sheisi Fonseca Leite da Silva Rocha, Carolina G. Olanda, Harold Hilarion Fokoue, Carlos Maurício R. Sant’Anna · 2019 · Current Topics in Medicinal Chemistry
5. Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein–protein Interactions
   Ercheng Wang, Gaoqi Weng, Huiyong Sun, Hongyan Du, Feng Zhu, Fu Chen, Zhe Wang, Tingjun Hou · 2019 · Physical Chemistry Chemical Physics
6. Prediction of physical protein–protein interactions
   András Szilágyi, Vera Grimm, Adrián K. Arakaki, Jeffrey Skolnick · 2005 · Physical Biology
7. FastContact: rapid estimate of contact and binding free energies
   Carlos Jaime Camacho, C. Zhang · 2005 · Computer applications in the biosciences
8. Humanized Affinity-matured Monoclonal Antibody 8H9 Has Potent Antitumor Activity and Binds to FG Loop of Tumor Antigen B7-H3
   Mahiuddin Ahmed, Ming Huei Cheng, Qi Zhao, Yehuda Goldgur, Sarah M. Cheal, Hong-Fen Guo, Steven M. Larson, Nai‐Kong V. Cheung · 2015 · Journal of Biological Chemistry
9. Antioxidant activity and anti-proliferative effect of a bioactive peptide from chickpea (Cicer arietinum L.)
   Zhaohui Xue, Haichao Wen, Lijuan Zhai, Yanqing Yu, Yanni Li, Wancong Yu, Aiqing Cheng, Cen Wang, Xiaohong Kou · 2015 · Food Research International
10. The scoring of poses in protein-protein docking: current capabilities and future directions
    Iain H. Moal, Mieczyslaw Torchala, Paul A. Bates, Juan Fernández‐Recio · 2013 · BMC Bioinformatics
11. Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies
    Rahmad Akbar, Habib Bashour, Puneet Rawat, Philippe Auguste Robert, Eva Smorodina, Tudor‐Stefan Cotet, Karine Flem Karlsen, Robert Frank, Brij Bhushan Mehta, Mai Ha Vu et al. · 2022 · mAbs
12. Pirin is an iron-dependent redox regulator of NF-κB
    Fange Liu, Imran Rehmani, Shingo Esaki, Rong Fu, Lirong Chen, Vesna Sator de Serrano, Aimin Liu · 2013 · Proceedings of the National Academy of Sciences
13. ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5
    Kevin J. Wiehe, Brian G. Pierce, Julian Mintseris, Wei Wei Tong, Robert Anderson, Rong Chen, Zhiping Weng · 2005 · Proteins Structure Function and Bioinformatics
14. The heads of the measles virus attachment protein move to transmit the fusion-triggering signal
    Chanakha K. Navaratnarajah, Numan Oezguen, Levi J. Rupp, Leah Kay, Vincent H. J. Léonard, Werner A. Braun, Roberto Cattaneo · 2011 · Nature Structural & Molecular Biology
15. Molecular Interplay between Endostatin, Integrins, and Heparan Sulfate
    Clément Faye, Christophe Moreau, Émilie Chautard, Reidunn Jetne Edelmann, Naomi Fukai, Florence Ruggiero, Martin James Humphries, Bjorn Reino Olsen, Sylvie Ricard‐Blum · 2009 · Journal of Biological Chemistry
16. Protein–protein docking: is the glass half-full or half-empty?
    Sándor Vajda, Carlos Jaime Camacho · 2004 · Trends in biotechnology
17. Integrative computational modeling of protein interactions
    João Rodrigues, Alexandre M. J. J. Bonvin · 2014 · FEBS Journal
18. I-TASSER gateway: A protein structure and function prediction server powered by XSEDE
    Wei Hui Zheng, Chengxin Zhang, Eric W. Bell, Yang Zhang · 2019 · Future Generation Computer Systems
19. xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein
    Bo Chen, Xingyi Cheng, Pan Li, Yangli-Ao Geng, Jing Gong, Shen Li, Zhi-Lei Bei, Xu Tan, Boyan Wang, Xin Zeng et al. · 2024 · bioRxiv
20. Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking
    Sheng‐You Huang · 2015 · Drug Discovery Today
21. Hot-spot analysis for drug discovery targeting protein-protein interactions
    Rosell, Mireia, Fernández-Recio, Juan · 2018 · Expert Opinion on Drug Discovery
22. DeepBindRG: a deep learning based method for estimating effective protein–ligand affinity
    Haiping Zhang, Linbu Liao, Konda Mani Saravanan, Peng Yin, Yanjie Wei · 2019 · PeerJ
23. Probing the Initial Stage of Aggregation of the Aβ10-35-protein: Assessing the Propensity for Peptide Dimerization
    Bogdan Tarus, John E. Straub, Dave Thirumalai · 2004 · Journal of Molecular Biology
24. Computational Approaches to Predict Protein–Protein Interactions in Crowded Cellular Environments
    Greta Grassmann, Mattia Miotto, Fausta Desantis, Lorenzo Di Rienzo, Gian Gaetano Tartaglia, Annalisa Pastore, Giancarlo Ruocco, Michele M. Monti, Edoardo Milanetti · 2024 · Chemical Reviews
25. Structure Function Analysis of an ADP-ribosyltransferase Type III Effector and Its RNA-binding Target in Plant Immunity
    Byeong‐ryool Jeong, Yan Lin, Anna Joe, Ming Guo, Christin Korneli, Huirong Yang, Ping Wang, Min Yu, Ronald L. Cerny, Dorothee Staiger et al. · 2011 · Journal of Biological Chemistry
26. Bio-Inspired Algorithms Applied to Molecular Docking Simulations
    Graziela Heberlé, Walter Filgueira de Azevedo · 2011 · Current Medicinal Chemistry
27. Peptide-Based Vaccines for Tuberculosis
    Wenping Gong, Chao Pan, Peng Cheng, Jie Wang, Guangyu Zhao, Xueqiong Wu · 2022 · Frontiers in Immunology
28. Biomacromolecular quantitative structure–activity relationship (BioQSAR): a proof-of-concept study on the modeling, prediction and interpretation of protein–protein binding affinity
    Peng Zhou, Congcong Wang, Feifei Tian, Yanrong Ren, Chao Yang, Jian Hua Huang · 2013 · Journal of Computer-Aided Molecular Design
29. Potential for Protein Surface Shape Analysis Using Spherical Harmonics and 3D Zernike Descriptors
    Vishwesh Venkatraman, Lee Sael, Daisuke Kihara · 2009 · Cell Biochemistry and Biophysics
30. Identification of a Potential Peptide Inhibitor of SARS-CoV-2 Targeting its Entry into the Host Cells
    Mirza S. Baig, Manikandan Alagumuthu, Sajjan Rajpoot, Uzma Saqib · 2020 · Drugs in R&D
31. Nucleolar protein Spindlin1 recognizes H3K4 methylation and stimulates the expression of rRNA genes
    Weixiang Wang, Zhi Chen, Zhuo Mao, Huihui Zhang, Xiaojun Ding, She Chen, Xiaodong Zhang, Rui-Ming Xu, Bing Zhu · 2011 · EMBO Reports
32. Comparing performance and energy efficiency of FPGAs and GPUs for high productivity computing
    Brahim Betkaoui, David Barrie Thomas, Wayne W. Luk · 2010 · International Conference on Field-Programmable Technology (FPT)
33. TNFR2 Stimulation Promotes Mitochondrial Fusion via Stat3- and NF-kB–Dependent Activation of OPA1 Expression
    Jinliang Nan, Hengxun Hu, Yong Sun, Lianlian Zhu, Yingchao Wang, Zhiwei Zhong, Jing Zhao, Na Zhang, Ya Wang, Yaping Wang et al. · 2017 · Circulation Research
34. FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking
    Efrat Mashiach, Ruth Nussinov, Haim J. Wolfson · 2010 · Nucleic Acids Research
35. The Crystal Structure of BamB Suggests Interactions with BamA and Its Role within the BAM Complex
    Nicholas Noinaj, J.W. Fairman, Susan K. Buchanan · 2011 · Journal of Molecular Biology
36. Computational design of Candida boidinii xylose reductase for altered cofactor specificity
    George A. Khoury, Hossein Fazelinia, Jonathan W. Chin, Robert J. Pantazes, Patrick C. Cirino, Costas D. Maranas · 2009 · Protein Science
37. Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors
    Rushikesh V. Sable, Seetharama D. S. Jois · 2015 · Molecules
38. Multi‐LZerD: Multiple protein docking for asymmetric complexes
    Juan Esquivel‐Rodríguez, Yifeng David Yang, Daisuke Kihara · 2012 · Proteins Structure Function and Bioinformatics
39. Mechanistic Insight into Human ether-à-go-go-related Gene (hERG) K+ Channel Deactivation Gating from the Solution Structure of the EAG Domain
    Frederick W. Muskett, Samrat Thouta, Steven J. Thomson, Alexander Bowen, Phillip James Stansfeld, John S. Mitcheson · 2010 · Journal of Biological Chemistry
40. Present and future challenges and limitations in protein–protein docking
    Carles Pons, Solène Grosdidier, Albert Solernou, Laura Pérez‐Cano, Juan Fernández‐Recio · 2009 · Proteins Structure Function and Bioinformatics
41. InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution
    Jessica Andréani, Guilhem Faure, Raphaël Guérois · 2013 · Bioinformatics
42. Computational Approaches to Toll-Like Receptor 4 Modulation
    Jean‐Marc Billod, Alessandra Lacetera, Joan Guzman‐Caldentey, Sonsoles Martín‐Santamaría · 2016 · Molecules
43. Characterization of local geometry of protein surfaces with the visibility criterion
    Bin Li, Srinivasan Turuvekere, Manish Agrawal, David La, Karthik Ramani A, Daisuke Kihara · 2007 · Proteins Structure Function and Bioinformatics
44. Integrating atom‐based and residue‐based scoring functions for protein–protein docking
    Thom Vreven, Howook Hwang, Zhiping Weng · 2011 · Protein Science
45. Accounting for loop flexibility during protein–protein docking
    Karine Bastard, Chantal Prévost, Martin Zacharias · 2005 · Proteins Structure Function and Bioinformatics
46. Molecular Modeling-Based Evaluation of hTLR10 and Identification of Potential Ligands in Toll-Like Receptor Signaling
    Rajiv Gandhi Govindaraj, Balachandran Manavalan, Gwang Lee, Sangdun Choi · 2010 · PLoS ONE
47. MDockPP: A hierarchical approach for protein‐protein docking and its application to CAPRI rounds 15–19
    Sheng‐You Huang, Xiaoqin Zou · 2010 · Proteins Structure Function and Bioinformatics
48. Computational Identification of Inhibitors of Protein-Protein Interactions
    Shijun Zhong, Alba T. Macias, Alexander D. MacKerell · 2006 · Current Topics in Medicinal Chemistry
49. ClusPro: Performance in CAPRI rounds 6–11 and the new server
    Stephen R. Comeau, Dima Kozakov, Ryan Brenke, Yang Shen, Dmitri Beglov, Sándor Vajda · 2007 · Proteins Structure Function and Bioinformatics
50. Crosstalk between the Akt/mTORC1 and NF-κB signaling pathways promotes hypoxia-induced pulmonary hypertension by increasing DPP4 expression in PASMCs
    Ying Li, Yang Li, Liang Dong, Zhiwei Yang, Jing Zhang, Shengli Zhang, Mengjie Niu, Jingwen Xia, Yi Gong, Ning Zhu et al. · 2019 · Acta Pharmacologica Sinica
51. ZDOCK predictions for the CAPRI challenge
    Rong Chen, Weiwei Tong, Julian Mintseris, Li Li, Zhiping Weng · 2003 · Proteins Structure Function and Bioinformatics
52. Eritoran inhibits S100A8-mediated TLR4/MD-2 activation and tumor growth by changing the immune microenvironment
    Atsuko Deguchi, Takeshi Tomita, Umeharu Ohto, Kazuhiro Takemura, Akio Kitao, Sachiko Akashi‐Takamura, Kensuke Miyake, Yoshiro Maru · 2015 · Oncogene
53. Metabolic switch regulates lineage plasticity and induces synthetic lethality in triple-negative breast cancer
    Yingsheng Zhang, Meng‐Ju Wu, Wan-Chi Lu, Yi‐Chuan Li, Chun Ju Chang, Jer‐Yen Yang · 2024 · Cell Metabolism
54. Mapping of discontinuous conformational epitopes by amide hydrogen/deuterium exchange mass spectrometry and computational docking
    Deepangi Pandit, Steven J. Tuske, Stephen J. Coales, Sook Yen E, Anita Liu, Jessica E. Lee, Jeffrey A. Morrow, Jennifer F. Nemeth, Yoshitomo Hamuro · 2012 · Journal of Molecular Recognition
55. Mapping Monomeric Threading to Protein–Protein Structure Prediction
    Guerler, Aysam, Govindarajoo, Brandon, Zhang, Yang · 2013 · Journal of Chemical Information and Modeling
56. Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery
    Wiktoria Wilman, Sonia Wróbel, Weronika Bielska, Piotr Deszyński, Paweł Dudzic, Igor Jaszczyszyn, Jędrzej Kaniewski, Jakub Młokosiewicz, Anahita Rouyan, Tadeusz Satława et al. · 2022 · Briefings in Bioinformatics
57. Pulsed EPR Determination of the Distance between Heme Iron and FMN Centers in a Human Inducible Nitric Oxide Synthase
    Andrei V. Astashkin, Bradley O. Elmore, Weihong Fan, Joseph Guy Guillemette, Changjian Feng · 2010 · Journal of the American Chemical Society
58. Computational design of epitope-specific functional antibodies
    Nimrod, Guy, Fischman, Sharon, Austin, Mark, Herman, Asael, Keyes, Feenagh, Leiderman, Olga, Hargreaves, David, Strajbl, Marek, Breed, Jason, Klompus, Shelley et al. · 2018 · Cell Reports
59. The Acute-Phase Protein Orosomucoid Regulates Food Intake and Energy Homeostasis via Leptin Receptor Signaling Pathway
    Yang Sun, Yili Yang, Zhen Qin, Jinya Cai, Xiu-Ming Guo, Yun Tang, Jingjing Wan, Ding‐Feng Su, Xia Liu · 2016 · Diabetes
60. Prediction of protein–protein binding free energies
    Thom Vreven, Howook Hwang, Brian G. Pierce, Zhiping Weng · 2012 · Protein Science
61. Update 1 of: Computational Modeling Approaches to Structure–Function Analysis of G Protein-Coupled Receptors
    Francesca Fanelli, Pier Giuseppe De Benedetti · 2011 · Chemical Reviews
62. Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens
    Federica Guarra, Giorgio Colombo · 2023 · Journal of Chemical Theory and Computation
63. The Glove-like Structure of the Conserved Membrane Protein TatC Provides Insight into Signal Sequence Recognition in Twin-Arginine Translocation
    Sureshkumar Ramasamy, Ravinder Abrol, Christian J. M. Suloway, William Clemons · 2013 · Structure
64. Sampling and scoring: A marriage made in heaven
    Sándor Vajda, David R. Hall, Dima Kozakov · 2013 · Proteins Structure Function and Bioinformatics
65. Green Fluorescent Protein Impairs Actin-Myosin Interactions by Binding to the Actin-binding Site of Myosin
    Onnik Agbulut, Alexis Huet, Nicolas J. Niederländer, Michel Pucéat, Philippe Menasché, Catherine Coirault · 2007 · Journal of Biological Chemistry
66. Structures of the multicomponent Rieske non-heme iron toluene 2,3-dioxygenase enzyme system
    Rosmarie Friemann, Kyoung Lee, Eric N. Brown, David Templeton Gibson, Hans Eklund, Subramanian Ramaswamy · 2008 · Acta Crystallographica Section D Biological Crystallography
67. Protein docking prediction using predicted protein-protein interface
    Bin Li, Daisuke Kihara · 2012 · BMC Bioinformatics
68. Cold-Active Winter Rye Glucanases with Ice-Binding Capacity
    Mahmoud W. F. Yaish, Andrew C. Doxey, Brendan J. McConkey, Barbara A. Moffatt, Marilyn Griffith · 2006 · PLANT PHYSIOLOGY
69. Human frataxin: iron and ferrochelatase binding surface
    Krisztina Z. Bencze, Taejin Yoon, César Millán‐Pacheco, Patrick B. Bradley, Nina Pastor, James Allan Cowan, Timothy L. Stemmler · 2007 · Chemical Communications
70. Molecular dynamics simulation of lentinan and its interaction with the innate receptor dectin-1
    Xiucong Wu, Ziming Zheng, Tingting Guo, Kaiping Wang, Yu Zhang · 2021 · International Journal of Biological Macromolecules
71. Automated and Efficient Generation of General Molecular Aggregate Structures
    Christoph Plett, Stefan Grimme · 2022 · Angewandte Chemie International Edition
72. Performance of ZDOCK and ZRANK in CAPRI rounds 13–19
    Howook Hwang, Thom Vreven, Brian G. Pierce, Jui‐Hung Hung, Zhiping Weng · 2010 · Proteins Structure Function and Bioinformatics
73. Synaptotagmin C2A loop 2 mediates Ca2+-dependent SNARE interactions essential for Ca2+-triggered vesicle exocytosis.
    Kara L. Lynch, Roy R L Gerona, E. C. Larsen, R. Marcia, Julie C. Mitchell, T. Martin · 2007 · Molecular Biology of the Cell
74. Computational tools for aptamer identification and optimization
    Di Sun, Miao Sun, Jialü Zhang, Xin Lin, Yinkun Zhang, Fanghe Lin, Peng Zhang, Chaoyong James Yang, Jia Tao Song · 2022 · TrAC Trends in Analytical Chemistry
75. Computational Docking of Antibody-Antigen Complexes, Opportunities and Pitfalls Illustrated by Influenza Hemagglutinin
    Mattia Pedotti, Luca Simonelli, Elsa Livoti, Luca Varani · 2011 · International Journal of Molecular Sciences
76. Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures.
    Shruthi Viswanath, Ilan E. Chemmama, Peter Cimermancic, A. Sali · 2017 · Biophysical Journal
77. In silico approach for Post-SELEX DNA aptamers: A mini-review
    Nor Azlina Ahmad, Razauden Mohamed Zulkifli, Huszalina Hussin, Muhammad Helmi Nadri · 2021 · Journal of Molecular Graphics and Modelling
78. Automated docking for novel drug discovery
    Martiniano Bello, Marlet Martínez‐Archundia, José Correa‐Basurto · 2013 · Expert Opinion on Drug Discovery
79. MEGADOCK: An All-to-All Protein-Protein Interaction Prediction System Using Tertiary Structure Data
    Masahito Ohue, Yuri Matsuzaki, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama · 2013 · Protein and Peptide Letters
80. A Review of Deep Learning Methods for Antibodies
    Jordan Graves, Jacob Byerly, Eduardo Priego, Naren Makkapati, S. Parish, Brenda P. Medellin, Monica Berrondo · 2020 · Antibodies
81. Biochemical characteristics and inhibitor selectivity of mouse indoleamine 2,3-dioxygenase-2
    Christopher J. D. Austin, B. M. Mailu, G. Maghzal, Á. Sánchez-Pérez, S. Rahlfs, K. Zocher, H. Yuasa, Jonathan W. Arthur, K. Becker, R. Stocker et al. · 2010 · Amino Acids
82. Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes
    Shoshana J. Wodak, Sándor Vajda, Marc Ferdinand Lensink, Dima Kozakov, Paul A. Bates · 2023 · Annual Review of Biophysics
83. Structure of the Preamyloid Dimer of β-2-Microglobulin from Covalent Labeling and Mass Spectrometry
    Vanessa Leah Mendoza, Kwasi Antwi, Mario Alberto Barón-Rodríguez, Cristian Blanco‐Tirado, Richard W. Vachet · 2010 · Biochemistry
84. Bound Water at Protein-Protein Interfaces: Partners, Roles and Hydrophobic Bubbles as a Conserved Motif
    Mostafa H. Ahmed, Francesca Spyrakis, Pietro Cozzini, Kumar Parijat Tripathi, Andrea Mozzarelli, J.N. Scarsdale, Martin K. Safo, Glen E. Kellogg · 2011 · PLoS ONE
85. Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments
    Roberto Mosca, Carles Pons, Juan Fernández‐Recio, Patrick Aloy · 2009 · PLoS Computational Biology
86. A review of the current trends in computational approaches in drug design and metabolism
    Russell B. O. Ouma, Silas M. Ngari, Joshua Kiprotich Kibet · 2024 · Discover Public Health
87. Insights into the Structural Basis of the GADD45β-mediated Inactivation of the JNK Kinase, MKK7/JNKK2
    Salvatore Papa, Simona Maria Monti, Rosa Maria Vitale, Concetta Bubici, Shanthi Jayawardena, Kellean Alvarez, Enrico De Smaele, Nina Alayne Dathan, Carlo Pedone, Menotti Ruvo et al. · 2007 · Journal of Biological Chemistry
88. Coarse-grained modeling of RNA 3D structure
    Wayne Dawson, Maciej Maciejczyk, Elzbieta J. Jankowska, Janusz Marek Bujnicki · 2016 · Methods
89. Bandwidth intensive 3-D FFT kernel for GPUs using CUDA
    Akira Nukada, Yasuhiko Ogata, Toshio Endo, Satoshi Matsuoka · 2008 · International Conference for High Performance Computing, Networking, Storage and Analysis (SC)
90. The TFIIF-Like Rpc37/53 Dimer Lies at the Center of a Protein Network To Connect TFIIIC, Bdp1, and the RNA Polymerase III Active Center
    Colin Chih‐Chien Wu, Yu‐Chun Lin, Hung‐Ta Chen · 2011 · Molecular and Cellular Biology
91. Inhibition of Toll-like receptors TLR4 and 7 signaling pathways by SIGIRR: A computational approach
    Jing Gong, Tiandi Wei, Robert W. Stark, Ferdinand Jamitzky, Wolfgang M. Heckl, Hans‐Joachim Anders, Maciej Lech, Shaila C. Rössle · 2009 · Journal of Structural Biology
92. Lebein, a snake venom disintegrin, suppresses human colon cancer cells proliferation and tumor-induced angiogenesis through cell cycle arrest, apoptosis induction and inhibition of VEGF expression
    Ons Zakraoui, Cezary Marcinkiewicz, Zohra Aloui, Houcemeddine Othman, Renaud Grépin, Meriam Haoues, Makram Essafi, Najet Srairi‐Abid, Ammar Gasmi, Habib Karoui et al. · 2016 · Molecular Carcinogenesis
93. How repertoire data are changing antibody science
    Claire Marks, Charlotte Mary Deane · 2020 · Journal of Biological Chemistry
94. Flexible protein docking refinement using pose‐dependent normal mode analysis
    Vishwesh Venkatraman, David W. Ritchie · 2012 · Proteins Structure Function and Bioinformatics
95. Binding Site and Inhibitory Mechanism of the Mambalgin-2 Pain-relieving Peptide on Acid-sensing Ion Channel 1a
    Miguel Salinas, Thomas Besson, Quentin Delettre, Sylvie Diochot, Sonia Boulakirba, Dominique Douguet, Éric Lingueglia · 2014 · Journal of Biological Chemistry
96. Redesign of a cross-reactive antibody to dengue virus with broad-spectrum activity and increased in vivo potency
    Kannan Tharakaraman, Luke N. Robinson, Andrew Hatas, Yi‐Ling Chen, Liu Siyue, S. Raguram, Viswanathan Sasisekharan, Gerald N. Wogan, Ram Sasisekharan · 2013 · Proceedings of the National Academy of Sciences
97. The performance of ZDOCK and ZRANK in rounds 6–11 of CAPRI
    Kevin J. Wiehe, Brian G. Pierce, Wei Wei Tong, Howook Hwang, Julian Mintseris, Zhiping Weng · 2007 · Proteins Structure Function and Bioinformatics
98. NLDock: a Fast Nucleic Acid–Ligand Docking Algorithm for Modeling RNA/DNA–Ligand Complexes
    Yuyu Feng, Keqiong Zhang, Qilong Wu, Sheng‐You Huang · 2021 · Journal of Chemical Information and Modeling
99. Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination
    Ryan E. Pavlovicz, Hahnbeom Park, F. DiMaio · 2019 · bioRxiv
100. Truncated human angiotensin converting enzyme 2; a potential inhibitor of SARS-CoV-2 spike glycoprotein and potent COVID-19 therapeutic agent
     Abdul Basit, Tanveer Ali, Shafiq ur Rehman · 2020 · Journal of Biomolecular Structure and Dynamics