CAPRI: A Critical Assessment of PRedicted Interactions

Cited by (705)

Items 301–400 of 705

1. Protein-ensemble–RNA docking by efficient consideration of protein flexibility through homology models
   Jiahua He, Huanyu Tao, Sheng‐You Huang · 2019 · Bioinformatics
2. IN SILICO SCREENING OF PROTEIN–PROTEIN INTERACTIONS WITH ALL-TO-ALL RIGID DOCKING AND CLUSTERING: AN APPLICATION TO PATHWAY ANALYSIS
   Yuri Matsuzaki, Yusuke Matsuzaki, Toshiyuki Sato, Yutaka Akiyama · 2009 · Journal of Bioinformatics and Computational Biology
3. The SKE‐DOCK server and human teams based on a combined method of shape complementarity and free energy estimation
   Genki Terashi, Mayuko Takeda‐Shitaka, Kazuhiko Kanou, Mitsuo Iwadate, Daisuke Takaya, Hideaki Umeyama · 2007 · Proteins Structure Function and Bioinformatics
4. Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach
   Isaure Chauvot de Beauchêne, Sjoerd J. de Vries, Martin Zacharias · 2016 · PLoS Computational Biology
5. Protein-RNA Docking Using ICM
   Yelena A. Arnautova, Ruben A Abagyan, Maxim M. Totrov · 2018 · Journal of Chemical Theory and Computation
6. Charged residues at protein interaction interfaces: Unexpected conservation and orchestrated divergence
   Nan Zhao, Bin Pang, Chi‐Ren Shyu, Dmitry Korkin · 2011 · Protein Science
7. The targets of CAPRI rounds 3–5
   Joël Janin · 2005 · Proteins Structure Function and Bioinformatics
8. Inhibition of the TIRAP-c-Jun interaction as a therapeutic strategy for AP1-mediated inflammatory responses
   Mansi Srivastava, Uzma Saqib, Sreeparna Banerjee, Kishore K. Wary, Burak Kizil, Kannan Muthu, Mirza S. Baig · 2019 · International Immunopharmacology
9. An Integrative Approach to the Study of Filamentous Oligomeric Assemblies, with Application to RecA
   Benjamin Boyer, Johann Ezelin, Pierre Poulain, Adrien Saladin, Martin Zacharias, Charles H. Robert, Chantal Prévost · 2015 · PLoS ONE
10. The 2010 cryo‐em modeling challenge
    Steven J. Ludtke, Catherine L. Lawson, Gerard J. Kleywegt, Helen Miriam Berman, Wah Chiu · 2012 · Biopolymers
11. IBC’s 22nd Annual Antibody Engineering and 9th Annual Antibody Therapeutics International Conferences and the 2011 Annual Meeting of The Antibody Society, December 5–8, 2011, San Diego, CA
    Johan Nilvebrant, D. Cameron Dunlop, Aroop Sircar, Thierry Wurch, Emilia Falkowska, Janice M. Reichert, Gustavo F. Helguera, Emily C. Piccione, Simon Brack, Sven Berger · 2012 · mAbs
12. Substrate channeling between the human dihydrofolate reductase and thymidylate synthase
    Nuo Wang, James Andrew McCammon · 2015 · Protein Science
13. Biophysical Aspect of Huntingtin Protein During polyQ: An In Silico Insight
    Chandrasekhar Gopalakrishnan, Shraddha Jethi, Namrata Kalsi, Rituraj Purohit · 2016 · Cell Biochemistry and Biophysics
14. Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems
    Didier Barradas‐Bautista, Mireia Rosell, Chiara Pallara, Juan Fernández‐Recio · 2017 · Advances in protein chemistry and structural biology
15. Dynamic perspectives into the mechanisms of mutation‐induced p53‐DNA binding loss and inactivation using active perturbation theory: Structural and molecular insights toward the design of potent reactivators in cancer therapy
    Fisayo Andrew Olotu, Mahmoud E. S. Soliman · 2018 · Journal of Cellular Biochemistry
16. Energy Landscape Analysis of Protein Dimers
    Yaakov Levy, Garegin A. Papoian, José N. Onuchic, Peter Guy Wolynes · 2004 · Israel Journal of Chemistry
17. Scoring a diverse set of high‐quality docked conformations: A metascore based on electrostatic and desolvation interactions
    Carlos Jaime Camacho, Hui Ma, P. Christoph Champ · 2006 · Proteins Structure Function and Bioinformatics
18. Prediction of Protein‐Protein Interactions
    Max Kotlyar, Andrea E.M. Rossos, Igor Jurišica · 2017 · Current Protocols in Bioinformatics
19. NUScon: a community-driven platform for quantitative evaluation of nonuniform sampling in NMR
    Yulia E. Pustovalova, Frank Delaglio, D. Levi Craft, Haribabu Arthanari, Ad Bax, Martin Billeter, Mark J. Bostock, Hesam Dashti, D. Flemming Hansen, Sven G. Hyberts et al. · 2021 · Magnetic Resonance
20. Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study
    Hugo Schweke, Qifang Xu, Gerardo Tauriello, Lorenzo Pantolini, Torsten F. Schwede, Frédéric Cazals, Alix Lhéritier, Juan Fernández‐Recio, Luis Angel Rodríguez‐Lumbreras, Ora Schueler‐Furman et al. · 2023 · PROTEOMICS
21. In silico protein function prediction: the rise of machine learning-based approaches
    Jiaxiao Chen, Zhonghui Gu, Luhua Lai, Jianfeng Pei · 2023 · Medical Review
22. Use of the “fuzzy oil drop” model to identify the complexation area in protein homodimers
    Mateusz Banach, Leszek Konieczny, Irena Roterman‐Konieczna · 2012 · Elsevier eBooks
23. Molecular Modeling of the Human Hemoglobin-Haptoglobin Complex Sheds Light on the Protective Mechanisms of Haptoglobin
    Chanin Nantasenamat, Virapong Prachayasittikul, Leif Bülow · 2013 · PLoS ONE
24. Networks of ProteinProtein Interactions: From Uncertainty to Molecular Details
    Javier Garcı́a-Garcı́a, Jaume Bonet, Emre Güney, Oriol Fornés, Joan Planas-Iglesias, Baldomero Oliva · 2012 · Molecular Informatics
25. Common physical basis of macromolecule-binding sites in proteins
    Yao Chi Chen, Carmay Lim · 2008 · Nucleic Acids Research
26. A correlation‐based method for the enhancement of scoring functions on funnel‐shaped energy landscapes
    Andrew W. Stumpff‐Kane, Michael Feig · 2006 · Proteins Structure Function and Bioinformatics
27. Structural prediction of protein interactions and docking using conservation and coevolution
    Jessica Andréani, Chloé Quignot, Raphaël Guérois · 2020 · Wiley Interdisciplinary Reviews Computational Molecular Science
28. Study on the molecular mechanism of inhibiting HIV-1 integrase by EBR28 peptide via molecular modeling approach
    Jianping Hu, Xin Qi Gong, Ji Guo Su, Wei Zu Chen, Cun Xin Wang · 2007 · Biophysical Chemistry
29. Adaptability in protein structures: structural dynamics and implications in ligand design
    Atanu Maity, Sarmistha Majumdar, Prerna Priya, Pallavi De, Sudipto Saha, Shubhra Ghosh Dastidar · 2014 · Journal of Biomolecular Structure and Dynamics
30. Blind Evaluation of Hybrid Protein Structure Analysis Methods based on Cross-Linking
    Adam Belsom, Michael Schneider, Oliver Brock, Juri Rappsilber · 2016 · Trends in Biochemical Sciences
31. Inclusion of the orientational entropic effect and low‐resolution experimental information for protein–protein docking in Critical Assessment of PRedicted Interactions (CAPRI)
    Sheng‐You Huang, Chengfei Yan, Sam Z. Grinter, Shan Chang, Lin Jiang, Xiaoqin Zou · 2013 · Proteins Structure Function and Bioinformatics
32. Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity
    Zhiqiang Yan, Jin Wang · 2013 · PLoS ONE
33. Combining H/D Exchange Mass Spectrometry and Computational Docking To Derive the Structure of Protein–Protein Complexes
    Victoria A. Roberts, Michael E. Pique, Simon Hsu, Sheng Li · 2017 · Biochemistry
34. Information-Driven Docking for TCR-pMHC Complex Prediction
    Thomas Peacock, Benny Chain · 2021 · Frontiers in Immunology
35. DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling
    Farhan Quadir, Raj S. Roy, Elham Soltanikazemi, Jianlin Cheng · 2021 · Frontiers in Molecular Biosciences
36. How does nitrous oxide reductase interact with its electron donors?—A docking study
    Kimmo Mattila, Tuomas Haltia · 2005 · Proteins Structure Function and Bioinformatics
37. Biological Units and their Effect upon the Properties and Prediction of Protein–Protein Interactions
    Emily Jefferson, Thomas P. Walsh, Geoffrey J. Barton · 2006 · Journal of Molecular Biology
38. Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20–27
    Krishna Praneeth Kilambi, Michael S. Pacella, Jianqing Xu, Jason W. Labonte, Justin R. Porter, Pravin Muthu, Kevin Drew, Daisuke Kuroda, Ora Schueler‐Furman, Richard Bonneau et al. · 2013 · Proteins Structure Function and Bioinformatics
39. Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy
    Huanyu Tao, Xuejun Zhao, Keqiong Zhang, Peicong Lin, Sheng‐You Huang · 2022 · Bioinformatics
40. DGCddG: Deep Graph Convolution for Predicting Protein-Protein Binding Affinity Changes Upon Mutations
    Yelu Jiang, Lijun Quan, Kailong Li, Yan Li, Yi Zhou, Tingfang Wu, Qiang Lyu · 2023 · IEEE Transactions on Computational Biology and Bioinformatics
41. Computational Modeling of Phosphotransfer Complexes in Two-Component Signaling
    Alexander H. Schug, Martin Weigt, James A. Hoch, José N. Onuchic, Terence Hwa B, Hendrik Szurmant · 2010 · Methods in enzymology on CD-ROM/Methods in enzymology
42. Improved performance in CAPRI round 37 using LZerD docking and template‐based modeling with combined scoring functions
    Lenna X. Peterson, Woong‐Hee Shin, Hyungrae Kim, Daisuke Kihara · 2017 · Proteins Structure Function and Bioinformatics
43. Determination of Ligand-Binding Sites on Proteins Using Long-Range Hydrophobic Potential
    Noriyuki Yamaotsu, Akifumi Oda, Shuichi Hirono · 2008 · Biological and Pharmaceutical Bulletin
44. The eNMR platform for structural biology
    Alexandre M. J. J. Bonvin, Antonio Rosato, Tsjerk A. Wassenaar · 2010 · Journal of Structural and Functional Genomics
45. A crowd-sourcing approach for the construction of species-specific cell signaling networks
    Erhan Bilal, Theodore Sakellaropoulos, Challenge Participants, Ioannis N. Melas, Dimitris E Messinis, Vincenzo Belcastro, Kahn Rhrissorrakrai, Pablo Meyer, Raquel Norel, Anita R. Iskandar et al. · 2014 · Bioinformatics
46. Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a
    Evelyne Deplazes, Josephine Davies, Alexandre M. J. J. Bonvin, Glenn F. King, Alan Edward Mark · 2015 · Journal of Chemical Information and Modeling
47. Protein social behavior makes a stronger signal for partner identification than surface geometry
    Élodie Laine, Alessandra Carbone · 2016 · Proteins Structure Function and Bioinformatics
48. Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist’s Perspective
    Fotis L. Kyrilis, Jaydeep Belapure, Panagiotis L. Kastritis · 2021 · Frontiers in Molecular Biosciences
49. Review and Comparative Analysis of Methods and Advancements in Predicting Protein Complex Structure
    Nan Zhao, Tong Wu, Wenda Wang, Lunchuan Zhang, Xinqi Gong · 2024 · Interdisciplinary Sciences Computational Life Sciences
50. Scoring docking conformations using predicted protein interfaces
    Reyhaneh Esmaielbeiki, Jean‐Christophe Nebel · 2014 · BMC Bioinformatics
51. SP-Dock: Protein-Protein Docking Using Shape and Physicochemical Complementarity
    Απόστολος Αξενόπουλος, Petros Daras, Georgios E. Papadopoulos, Elias N. Houstis · 2013 · IEEE Transactions on Computational Biology and Bioinformatics
52. Human and server docking prediction for CAPRI round 30‐35 using LZerD with combined scoring functions
    Lenna X. Peterson, Hyungrae Kim, Juan Esquivel‐Rodríguez, Amitava Roy, Xusi Han, Woong‐Hee Shin, Jian Zhang, Genki Terashi, Matt Lee, Daisuke Kihara · 2016 · Proteins Structure Function and Bioinformatics
53. Protein-assisted RNA fragment docking (RnaX) for modeling RNA–protein interactions using ModelX
    Javier Delgado, Leandro Radusky, Damiano Cianferoni, Luis G. Serrano · 2019 · Proceedings of the National Academy of Sciences
54. Combining interface core and whole interface descriptors in postscan processing of protein‐protein docking models
    Noga Kowalsman, Miriam Eisenstein · 2009 · Proteins Structure Function and Bioinformatics
55. Side‐chain rotamer transitions at protein‐protein interfaces
    Mainak Guharoy, Joël Janin, Charles H. Robert · 2010 · Proteins Structure Function and Bioinformatics
56. Protease-Inhibitor Interaction Predictions: Lessons on the Complexity of Protein–Protein Interactions
    Nikolaus Fortelny, Georgina S. Butler, Christopher M. Overall, Paul Pavlidis · 2017 · Molecular & Cellular Proteomics
57. Computational approaches to protein-protein interaction
    Giacomo Franzot, Oliviero Carugo · 2003 · Journal of Structural and Functional Genomics
58. A docking analysis of the statistical physics of protein–protein recognition
    Julie Bernauer, Anne Poupon B, Jérôme Azé, Joël Janin · 2005 · Physical Biology
59. Computational investigation of molecular mechanism and neuropathological implications in Huntington disease
    Chandrasekhar Gopalakrishnan, Namrata Kalsi, Shraddha Jethi, Rituraj Purohit · 2015 · Molecular and Cellular Biochemistry
60. Performance and enhancement of the LZerD protein assembly pipeline in CAPRI 38‐46
    Charles W. Christoffer, Genki Terashi, Woong‐Hee Shin, Tunde W. Aderinwale, Sai Raghavendra Maddhuri Venkata Subramaniya, Lenna X. Peterson, Jacob C. Verburgt, Daisuke Kihara · 2019 · Proteins Structure Function and Bioinformatics
61. Molecular Docking and Molecular Dynamics Study on the Effect of ERCC1 Deleterious Polymorphisms in ERCC1-XPF Heterodimer
    C. George Priya Doss, N. Nagasundaram · 2013 · Applied Biochemistry and Biotechnology
62. A close look at protein function prediction evaluation protocols
    Indika Kahanda, Christopher S. Funk, Fahad Ullah, Karin M. Verspoor, Asa Ben‐Hur · 2015 · GigaScience
63. Recent progress and future challenges in structure-based protein-protein interaction prediction
    Rongqing Yuan, Jing Zhang, Jian Zhou, Qian Cong · 2025 · Molecular Therapy
64. Computational Network Inference for Bacterial Interactomics
    Katherine James, José Muñoz-Muñoz · 2022 · mSystems
65. Intuitive, but not simple: Including explicit water molecules in protein–protein docking simulations improves model quality
    Hardik I. Parikh, Glen E. Kellogg · 2013 · Proteins Structure Function and Bioinformatics
66. Structural evaluation of BTK and PKCδ mediated phosphorylation of MAL at positions Tyr86 and Tyr106
    Rehan Zafar Paracha, Amjad Ali, Jamil Ahmad, Riaz Hussain, Umar H.K. Niazi, Syed Aun Muhammad · 2014 · Computational Biology and Chemistry
67. Predictive and Experimental Approaches for Elucidating Protein–Protein Interactions and Quaternary Structures
    John Nealon, Limcy S Philomina, Liam James McGuffin · 2017 · International Journal of Molecular Sciences
68. Identifying protein-protein interface via a novel multi-scale local sequence and structural representation
    Fei Guo, Quan Zou, Guang Yang, Dan Wang, Jijun Tang, Junhai Xu · 2019 · BMC Bioinformatics
69. Improved flexible refinement of protein docking in CAPRI rounds 22–27
    Yang Shen · 2013 · Proteins Structure Function and Bioinformatics
70. Native fold and docking pose discrimination by the same residue‐based scoring function
    Edoardo Sarti, Daniele Granata, Flavio Seno, Antonio Trovato, Alessandro Laio · 2015 · Proteins Structure Function and Bioinformatics
71. Performance of ZDOCK and IRAD in CAPRI rounds 28–34
    Thom Vreven, Brian G. Pierce, Tyler M. Borrman, Zhiping Weng · 2016 · Proteins Structure Function and Bioinformatics
72. Exploring the mechanistic insights of Cas scaffolding protein family member 4 with protein tyrosine kinase 2 in Alzheimer’s disease by evaluating protein interactions through molecular docking and dynamic simulations
    Mubashir Hassan, Saba Shahzadi, Hany Alashwal, Nazar Zaki, Sung‐Yum Seo, Ahmed A. Moustafa · 2018 · Neurological Sciences
73. An overview of data‐driven HADDOCK strategies in CAPRI rounds 38‐45
    Panagiotis I. Koukos, Jorge Roel‐Touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikael E. Trellet, Adrien S. J. Melquiond, Li C. Xue, Rodrigo V. Honorato, Irina Sousa Moreira et al. · 2019 · Proteins Structure Function and Bioinformatics
74. Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition
    Hui Xiao, Chun Hua Li, Long Zhu Shen, Xin Qi Gong, Wei Zu Chen, Cun Xin Wang · 2005 · Proteins Structure Function and Bioinformatics
75. Molecular Docking: State-of-the-Art Scoring Functions and Search Algorithms
    Rafaela Molina de Angelo, Daniel S. de Sousa, Aldineia P. da Silva, Laise P. A. Chiari, Albérico B. F. da Silva, Kathia Maria Honorio · 2024 · Computer-aided drug discovery and design
76. Proteome of the insulin-secreting Min6 cell porosome complex: Involvement of Hsp90 in its assembly and function
    Amulya Rajagopal, Sanjana Kulkarni, Kenneth T. Lewis, Xuequn Chen, Abir Maarouf Kabbani, Christopher V. Kelly, Douglas J. Taatjes, Bhanu P. Jena · 2014 · Journal of Proteomics
77. Assessing the energy landscape of CAPRI targets by FunHunt
    Nir London, Ora Schueler‐Furman · 2007 · Proteins Structure Function and Bioinformatics
78. FunHunt: model selection based on energy landscape characteristics
    Nir London, Ora Schueler‐Furman · 2008 · Biochemical Society Transactions
79. SimiCon: a web tool for protein–ligand model comparison through calculation of equivalent atomic contacts
    Manuel Rueda, Vsevolod Katritch, Eugene Raush, Ruben A Abagyan · 2010 · Bioinformatics
80. Computational Study for Protein-Protein Docking Using Global Optimization and Empirical Potentials
    Kyoungrim Lee · 2008 · International Journal of Molecular Sciences
81. Performance of MDockPP in CAPRI rounds 28‐29 and 31‐35 including the prediction of water‐mediated interactions
    Xianjin Xu, Liming Qiu, Chengfei Yan, Zhiwei Ma, Sam Z. Grinter, Xiaoqin Zou · 2016 · Proteins Structure Function and Bioinformatics
82. Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks
    Surabhi Maheshwari, Michał Bryliński · 2017 · BMC Bioinformatics
83. Docking protein domains in contact space
    Stefano Lise, Alice Walker-Taylor, David T. Jones · 2006 · BMC Bioinformatics
84. Recent advances in computational studies of GPCR-G protein interactions
    Jinan Wang, Yinglong Miao · 2019 · Advances in protein chemistry and structural biology
85. Protein-Protein Interfaces Are Special
    Ilya A. Vakser · 2004 · Structure
86. Protein‐protein docking by shape‐complementarity and property matching
    Tim Geppert, Ewgenij Proschak, Gisbert Schneider · 2010 · Journal of Computational Chemistry
87. Protein-Protein Docking Methods
    Garland R. Marshall, Ilya A. Vakser · 2006 · Springer eBooks
88. Missense variants in ACE2 are predicted to encourage and inhibit interaction with SARS-CoV-2 Spike and contribute to genetic risk in COVID-19
    Stuart A. MacGowan, Geoffrey J. Barton · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
89. Refinement of protein-protein complexes in contact map space with metadynamics simulations
    Pfeiffenberger, Erik, Bates, Paul A. · 2019 · Proteins Structure Function and Bioinformatics
90. Predicting Protein Dimer Structures Using MELD × MD
    Emiliano Brini, Dima Kozakov, Ken A. Dill · 2019 · Journal of Chemical Theory and Computation
91. Performance of ZDOCK and IRAD in CAPRI rounds 39‐45
    Thom Vreven, Sweta Vangaveti, Tyler M. Borrman, Jennifer C. Gaines, Zhiping Weng · 2020 · Proteins Structure Function and Bioinformatics
92. Challenges and opportunities of automated protein‐protein docking: HDOCK server vs human predictions in CAPRI Rounds 38‐46
    Yumeng Yan, Jiahua He, Yuyu Feng, Peicong Lin, Huanyu Tao, Sheng‐You Huang · 2020 · Proteins Structure Function and Bioinformatics
93. Insight into Molecular Interactions Between Two PB1 Domains
    Audrey van Drogen, Catherine Zwahlen, Matthias Peter, Alexandre M. J. J. Bonvin · 2004 · Journal of Molecular Biology
94. How the protonation state of a phosphorylated amino acid governs molecular recognition: insights from classical molecular dynamics simulations
    Raiji Kawade, Daisuke Kuroda, Kouhei Tsumoto · 2019 · FEBS Letters
95. Assembly of transmembrane helices of simple polytopic membrane proteins from sequence conservation patterns
    Yungki Park, Volkhard Helms · 2006 · Proteins Structure Function and Bioinformatics
96. Predicting protein–DNA interactions by full search computational docking
    Victoria A. Roberts, Michael E. Pique, Lynn F. Ten Eyck, Sheng Li · 2013 · Proteins Structure Function and Bioinformatics
97. Protein-Protein Docking Using Evolutionary Information
    Aravindan Arun Nadaradjane, Raphaël Guérois, Jessica Andréani · 2018 · Methods in molecular biology
98. Estimating structure quality trends in the Protein Data Bank by equivalent resolution
    Anurag Bagaria, Victor Jaravine, Peter Güntert · 2013 · Computational Biology and Chemistry
99. Study of protein–protein interaction using conformational space annealing
    Kyoungrim Lee, Jaehyun Sim, Jooyoung Lee · 2005 · Proteins Structure Function and Bioinformatics
100. Antiviral compound screening, peptide designing, and protein network construction of influenza a virus (strain a/Puerto Rico/8/1934 H1N1)
     Surovi Saikia, Manobjyoti Bordoloi, Rajeev Sarmah, Bhaskor Kolita · 2018 · Drug Development Research