CAPRI: A Critical Assessment of PRedicted Interactions

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Items 101–200 of 705

1. Macromolecular recognition in the Protein Data Bank
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2. Automated Protein Structure Homology Modeling: A Progress Report
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3. Network analysis and in silico prediction of protein–protein interactions with applications in drug discovery
   Yoichi Murakami, Lokesh P. Tripathi, Philip Prathipati, Kenji Mizuguchi · 2017 · Current Opinion in Structural Biology
4. Protein–protein docking: is the glass half-full or half-empty?
   Sándor Vajda, Carlos Jaime Camacho · 2004 · Trends in biotechnology
5. Integrative computational modeling of protein interactions
   João Rodrigues, Alexandre M. J. J. Bonvin · 2014 · FEBS Journal
6. Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D
   Aleksey Porollo, Jarek Meller · 2007 · BMC Bioinformatics
7. 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
8. Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how
   Nir London, Barak Raveh, Ora Schueler‐Furman · 2013 · Current Opinion in Structural Biology
9. Protein Docking Model Evaluation by Graph Neural Networks
   Xiao Wang, Sean T. Flannery, Daisuke Kihara · 2021 · Frontiers in Molecular Biosciences
10. Oligomeric protein structure networks: insights into protein-protein interactions
    K. V. Brinda, Saraswathi Vishveshwara · 2005 · BMC Bioinformatics
11. Geometric algorithms for the conformational analysis of long protein loops
    Juan Cortés, Thierry Siméon, Magali Remaud‐Siméon, Vinh Tran · 2004 · Journal of Computational Chemistry
12. Statistical Analysis of Interface Similarity in Crystals of Homologous Proteins
    Qifang Xu, Adrian A. Canutescu, Guoli Wang, Maxim V. Shapovalov, Zoran Obradovic A, Roland L. Dunbrack · 2008 · Journal of Molecular Biology
13. In silico Approaches for the Design and Optimization of Interfering Peptides Against Protein–Protein Interactions
    Zahra Sadat Hashemi, Mahboubeh Zarei, Mohsen Karami Fath, Mahmoud Ganji, Mahboube Shahrabi Farahani, Fatemeh Afsharnouri, Navid Pourzardosht, Bahman Khalesi, Abolfazl Jahangiri, Mohammad Reza Rahbar et al. · 2021 · Frontiers in Molecular Biosciences
14. Protein–protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach
    Özlem Keskin, Buyong Ma, Kristina Rogale, Kannan Gunasekaran, Ruth Nussinov · 2005 · Physical Biology
15. Progress in protein–protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side‐chain flexibility
    Ora Schueler‐Furman, Chu Wang, David A. Baker · 2005 · Proteins Structure Function and Bioinformatics
16. PPCheck: A Webserver for the Quantitative Analysis of Protein-Protein Interfaces and Prediction of Residue Hotspots
    Anshul Sukhwal, Ramanathan Sowdhamini · 2015 · Bioinformatics and Biology Insights
17. BIPSPI: a method for the prediction of partner-specific protein–protein interfaces
    Rubén Sánchez-García, Carlos Óscar S. Sorzano, J.M. Carazo, Joan Segura · 2018 · Bioinformatics
18. Modeling Antibody-Antigen Complexes by Information-Driven Docking
    Francesco Ambrosetti, Brian Jiménez‐García, Jorge Roel‐Touris, Alexandre M. J. J. Bonvin · 2019 · Structure
19. Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations
    Jinan Wang, Andrey Evgen'evich Alekseenko, Dima Kozakov, Yinglong Miao · 2019 · Frontiers in Molecular Biosciences
20. Towards a detailed atlas of protein–protein interactions
    Roberto Mosca, Tirso Pons, Arnaud Gerard Michel Ceol, Alfonso Valencia, Patrick Aloy · 2013 · Current Opinion in Structural Biology
21. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions
    Rocco Moretti, Sarel Jacob Fleishman, Rudi Agius, Mieczyslaw Torchala, Paul A. Bates, Panagiotis L. Kastritis, João Rodrigues, Mikael E. Trellet, Alexandre M. J. J. Bonvin, Meng Cui et al. · 2013 · Proteins Structure Function and Bioinformatics
22. Optimal protein‐RNA area, OPRA: A propensity‐based method to identify RNA‐binding sites on proteins
    Laura Pérez‐Cano, Juan Fernández‐Recio · 2009 · Proteins Structure Function and Bioinformatics
23. Integrative Modelling of Biomolecular Complexes
    Panagiotis I. Koukos, Alexandre M. J. J. Bonvin · 2019 · Journal of Molecular Biology
24. Prediction of Multimolecular Assemblies by Multiple Docking
    Yuval Inbar, Hadar Benyamini, Ruth Nussinov, Haim J. Wolfson · 2005 · Journal of Molecular Biology
25. Identification of the protein kinase A regulatory R I α-catalytic subunit interface by amide H/ 2 H exchange and protein docking
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26. Integrating atom‐based and residue‐based scoring functions for protein–protein docking
    Thom Vreven, Howook Hwang, Zhiping Weng · 2011 · Protein Science
27. Accounting for loop flexibility during protein–protein docking
    Karine Bastard, Chantal Prévost, Martin Zacharias · 2005 · Proteins Structure Function and Bioinformatics
28. Assessment of predictions submitted for the CASP7 domain prediction category
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29. 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
30. Computational Identification of Inhibitors of Protein-Protein Interactions
    Shijun Zhong, Alba T. Macias, Alexander D. MacKerell · 2006 · Current Topics in Medicinal Chemistry
31. iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations
    Geng, Cunliang, Vangone, Anna, Folkers, Gert E., Xue, Li C., Bonvin, Alexandre M. J. J. · 2019 · Proteins: Structure, Function, and Bioinformatics
32. Various strategies of using residual dipolar couplings in NMR‐driven protein docking: Application to Lys48‐linked di‐ubiquitin and validation against 15 N‐relaxation data
    Aalt D. J. van Dijk, David Fushman, Alexandre M. J. J. Bonvin · 2005 · Proteins Structure Function and Bioinformatics
33. Data‐driven docking: HADDOCK's adventures in CAPRI
    Aalt D. J. van Dijk, Sjoerd J. de Vries, Cyril Dominguez, Hebing Chen, Huan‐Xiang Zhou, Alexandre M. J. J. Bonvin · 2005 · Proteins Structure Function and Bioinformatics
34. Computational Prediction of Protein–Protein Interactions
    John C. Obenauer, Michael B. Yaffe · 2004 · Humana Press eBooks
35. Mapping Monomeric Threading to Protein–Protein Structure Prediction
    Guerler, Aysam, Govindarajoo, Brandon, Zhang, Yang · 2013 · Journal of Chemical Information and Modeling
36. Inhibiting transient protein–protein interactions: lessons from the Cdc25 protein tyrosine phosphatases
    Johannes Rudolph · 2007 · Nature reviews. Cancer
37. Determining Effects of Non-synonymous SNPs on Protein-Protein Interactions using Supervised and Semi-supervised Learning
    Nan Zhao, Jing Ginger Han, Chi‐Ren Shyu, Dmitry Korkin · 2014 · PLoS Computational Biology
38. Structural Analysis of Large Protein Complexes Using Solvent Paramagnetic Relaxation Enhancements
    Tobias Madl, Thomas Guettler, Dirk Görlich, Michael Sattler · 2011 · Angewandte Chemie International Edition
39. CASD-NMR: critical assessment of automated structure determination by NMR
    Antonio Rosato, Anurag Bagaria, David A. Baker, Benjamin Bardiaux, Andrea Cavalli, Jurgen F. Doreleijers, Andrea Giachetti, Paul Guerry, Peter Güntert, Torsten Herrmann et al. · 2009 · Nature Methods
40. Identification of Protein–Ligand Binding Sites by the Level-Set Variational Implicit-Solvent Approach
    Zuojun Guo, Bo Li, Li‐Tien Cheng, Shenggao Zhou, James Andrew McCammon, Jianwei Che · 2015 · Journal of Chemical Theory and Computation
41. Sampling and scoring: A marriage made in heaven
    Sándor Vajda, David R. Hall, Dima Kozakov · 2013 · Proteins Structure Function and Bioinformatics
42. Recent advances in user-friendly computational tools to engineer protein function
    Carlos Eduardo Sequeiros-Borja, Bartłomiej Surpeta, Jan Brezovský · 2020 · Briefings in Bioinformatics
43. Score_set: A CAPRI benchmark for scoring protein complexes
    Marc Ferdinand Lensink, Shoshana J. Wodak · 2014 · Proteins Structure Function and Bioinformatics
44. Protein docking prediction using predicted protein-protein interface
    Bin Li, Daisuke Kihara · 2012 · BMC Bioinformatics
45. 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
46. 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
47. Computational exploration of structural information from cryo-electron tomograms
    Achilleas S. Frangakis, Friedrich G. Förster · 2004 · Current Opinion in Structural Biology
48. False positive reduction in protein-protein interaction predictions using gene ontology annotations
    Mahmood Akhavan Mahdavi, Yen‐Han Lin · 2007 · BMC Bioinformatics
49. iScore: a novel graph kernel-based function for scoring protein–protein docking models
    Cunliang Geng, Yong Gyu Jung, Nicolas Renaud, Vasant Honavar, Alexandre M. J. J. Bonvin, Li C. Xue · 2019 · Bioinformatics
50. 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
51. Integrative Modeling of Biomolecular Complexes: HADDOCKing with Cryo-Electron Microscopy Data
    Gydo C. P. van Zundert, Adrien S. J. Melquiond, Alexandre M. J. J. Bonvin · 2015 · Structure
52. Supramolecular Structure and Function 7
    2001 · Springer eBooks
53. M-TASSER: An Algorithm for Protein Quaternary Structure Prediction
    Chen, Huiling, Skolnick, Jeffrey · 2008 · Biophysical Journal
54. Determining macromolecular assembly structures by molecular docking and fitting into an electron density map
    Keren Lasker, Andrej Šali, Haim J. Wolfson · 2010 · Proteins Structure Function and Bioinformatics
55. Identification of near‐native structures by clustering protein docking conformations
    Stephan Lorenzen, Yang Zhang · 2007 · Proteins Structure Function and Bioinformatics
56. Constructing structural networks of signaling pathways on the proteome scale
    Guray Kuzu, Özlem Keskin, Attila Gürsoy, Ruth Nussinov · 2012 · Current Opinion in Structural Biology
57. DDMut-PPI: predicting effects of mutations on protein–protein interactions using graph-based deep learning
    Yunzhuo Zhou, Yoochan Myung, Carlos H. M. Rodrigues, David Benjamin Ascher · 2024 · Nucleic Acids Research
58. Structure and Function of p53-DNA Complexes with Inactivation and Rescue Mutations: A Molecular Dynamics Simulation Study
    Balu Kamaraj, Annemie Bogaerts · 2015 · PLoS ONE
59. Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization
    Erik R. Lindahl · 2005 · Nucleic Acids Research
60. Defining the limits of homology modeling in information‐driven protein docking
    João Rodrigues, Adrien S. J. Melquiond, Ezgi Karaca, Mikael E. Trellet, Marc van Dijk, Gydo C. P. van Zundert, Christophe Schmitz, Sjoerd J. de Vries, Annalisa Bordogna, Laura Bonati et al. · 2013 · Proteins Structure Function and Bioinformatics
61. Prediction of protein–protein interactions: unifying evolution and structure at protein interfaces
    Nurcan Tunçbağ, Attila Gürsoy, Özlem Keskin · 2011 · Physical Biology
62. Testing computational prediction of missense mutation phenotypes: Functional characterization of 204 mutations of human cystathionine beta synthase
    Qiong Wei, Liqun Wang, Qiang Wang, Warren D. Kruger, Roland L. Dunbrack · 2010 · Proteins Structure Function and Bioinformatics
63. Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1
    Anna Vangone, João Rodrigues, Li C. Xue, Gydo C. P. van Zundert, Cunliang Geng, Zeynep Kurkcuoglu, Mehdi Nellen, Siddarth Narasimhan, Ezgi Karaca, Marc van Dijk et al. · 2016 · Proteins Structure Function and Bioinformatics
64. Advances to tackle backbone flexibility in protein docking
    Ameya Harmalkar, Jeffrey J. Gray · 2020 · Current Opinion in Structural Biology
65. Interpreting protein variant effects with computational predictors and deep mutational scanning
    Benjamin Livesey, Joseph A. Marsh · 2022 · Disease Models & Mechanisms
66. A new protein–protein docking scoring function based on interface residue properties
    Julie Bernauer, Jérôme Azé, Joël Janin, Anne Poupon · 2007 · Bioinformatics
67. HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry
    Yumeng Yan, Huanyu Tao, Sheng‐You Huang · 2018 · Nucleic Acids Research
68. Using protein binding site prediction to improve protein docking
    Bingding Huang, Michael Schroeder · 2008 · Gene
69. Trends in therapeutic antibody affinity maturation: From in-vitro towards next-generation sequencing approaches
    Maryam Tabasinezhad, Yeganeh Talebkhan, Wolfgang Wenzel, Hamzeh Rahimi, Eskandar Omidinia, Fereidoun Mahboudi · 2019 · Immunology Letters
70. SSIPe: accurately estimating protein–protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function
    Xiaoqiang Huang, Wei Hui Zheng, Robin Pearce, Yang Zhang · 2019 · Bioinformatics
71. CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock
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72. A nonredundant structure dataset for benchmarking protein‐RNA computational docking
    Sheng‐You Huang, Xiaoqin Zou · 2012 · Journal of Computational Chemistry
73. Assessment of predictions submitted for the CASP7 function prediction category
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74. Classification of protein complexes based on docking difficulty
    Sándor Vajda · 2005 · Proteins Structure Function and Bioinformatics
75. Integrative Structural Biology in the Era of Accurate Structure Prediction
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76. Attention mechanism enhanced LSTM with residual architecture and its application for protein-protein interaction residue pairs prediction
    Jiale Liu, Xinqi Gong · 2019 · BMC Bioinformatics
77. On Side-Chain Conformational Entropy of Proteins
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78. ClusPro-DC: dimer classification by the Cluspro server for protein–protein docking
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79. Evaluating native-like structures of RNA-protein complexes through the deep learning method
    Chengwei Zeng, Yiren Jian, Soroush Vosoughi, Chen Zeng, Yunjie Zhao · 2023 · Nature Communications
80. Exploring the Molecular Design of Protein Interaction Sites with Molecular Dynamics Simulations and Free Energy Calculations
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81. GalaxyTongDock: Symmetric and asymmetric ab initio protein–protein docking web server with improved energy parameters
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82. Improving Protein–Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM–GBSA Scoring Function
    Huanyu Tao, Yanjun Zhang, Sheng‐You Huang · 2020 · Journal of Chemical Information and Modeling
83. Proposed structural models of the prothrombinase (FXa–FVa) complex
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84. Protein structural bioinformatics: An overview
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85. New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces
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86. Biophysical aspect of phosphatidylinositol 3-kinase and role of oncogenic mutants (E542K & E545K)
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87. Computational modeling of protein assemblies
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88. HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures
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89. A simple reference state makes a significant improvement in near‐native selections from structurally refined docking decoys
    Shide Liang, Song Liu, Chi Zhang, Yaoqi Zhou · 2007 · Proteins Structure Function and Bioinformatics
90. Low-resolution structure refinement in electron microscopy
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91. A protein‐RNA docking benchmark (II): Extended set from experimental and homology modeling data
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92. In Silico Carborane Docking to Proteins and Potential Drug Targets
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93. Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood
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94. Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue
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95. Predicting oligomeric assemblies: N-mers a primer
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96. The impact of <scp>AI</scp> ‐based modeling on the accuracy of protein assembly prediction: Insights from <scp>CASP15</scp>
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97. Screening of Protein–Protein Interaction Modulators via Sulfo-Click Kinetic Target-Guided Synthesis
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98. The Third CAPRI Assessment Meeting Toronto, Canada, April 20–21, 2007
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99. What in silico molecular docking can do for the ‘bench-working biologists’
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100. On proteins, grids, correlations, and docking
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