Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition

Lensink, Marc F., Velankar, Sameer, Wodak, Shoshana J.·2017·Proteins Structure Function and Bioinformatics

Cited by (222)

Items 101–200 of 222

  1. ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking
    Mikhail Ignatov, Andrey Maksimovich Kazennov, Dima Kozakov · 2018 · Journal of Molecular Biology
  2. 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
  3. Benchmarking AlphaFold3-like Methods for Protein-Peptide Complex Prediction
    Fan Zhou, Shangwei Guo, Xiangda Peng, Shuhan Zhang, Cuicui Men, Xiaobo Duan, Guoliang Zhu, Zechen Wang, Weifeng Li, Yuguang Mu et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  4. Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis
    Zhou, Tian-ming, Wang, Sheng, Xu, Jinbo · 2017
  5. Modeling EphB4-EphrinB2 protein–protein interaction using flexible docking of a short linear motif
    Maciej Paweł Ciemny, Mateusz Kurciński, Maciej Błaszczyk, Andrzej Koliński, Sebastian Kmiecik · 2017 · BioMedical Engineering OnLine
  6. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)
    Christine Anne Orengo, Sameer S Velankar, Shoshana J. Wodak, Vincent Zoete, Alexandre M. J. J. Bonvin, Arne Elofsson, K. Anton Feenstra, Dietland L. Gerloff, Thomas Hamelryck, John M. Hancock et al. · 2020 · F1000Research
  7. Update of the ATTRACT force field for the prediction of protein-protein binding affinity
    Jean-Baptiste Chéron, Martin Zacharias, Serge Antonczak, Sébastien Fiorucci · 2017 · Journal of Computational Chemistry
  8. Predicting Protein Dimer Structures Using MELD × MD
    Emiliano Brini, Dima Kozakov, Ken A. Dill · 2019 · Journal of Chemical Theory and Computation
  9. Modeling beta‐sheet peptide‐protein interactions: Rosetta FlexPepDock in CAPRI rounds 38‐45
    Alisa Khramushin, Orly Marcu, Nawsad Alam, Orly Shimony, Dzmitry Padhorny, Emiliano Brini, Ken A. Dill, Sándor Vajda, Dima Kozakov, Ora Schueler‐Furman · 2019 · Proteins Structure Function and Bioinformatics
  10. 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
  11. 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
  12. Transmembrane Protein Docking with JabberDock
    Lucas S. P. Rudden, Matteo T. Degiacomi · 2021 · Journal of Chemical Information and Modeling
  13. Computational approaches to macromolecular interactions in the cell
    Ilya A. Vakser, Eric J. Deeds · 2019 · Current Opinion in Structural Biology
  14. Protein-Protein Docking Using Evolutionary Information
    Aravindan Arun Nadaradjane, Raphaël Guérois, Jessica Andréani · 2018 · Methods in molecular biology
  15. A knowledge-based scoring function to assess quaternary associations of proteins
    Abhilesh S Dhawanjewar, Ankit Roy, Mallur Srivatsan Madhusudhan · 2020 · Bioinformatics
  16. Protein–ligand docking using FFT based sampling: D3R case study
    Dzmitry Padhorny, David R. Hall, Hanieh Mirzaei, Artem B. Mamonov, Mohammad Moghadasi, Andrey Evgen'evich Alekseenko, Dmitri Beglov, Dima Kozakov · 2017 · Journal of Computer-Aided Molecular Design
  17. The Inclusion of Water Molecules in Residue Interaction Networks Identifies Additional Central Residues
    Guillaume Brysbaert, Ralf Blossey, Marc Ferdinand Lensink · 2018 · Frontiers in Molecular Biosciences
  18. GroScore: Accurate Scoring of Protein–Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations
    Jan Walther Perthold, Chris Oostenbrink · 2019 · Journal of Chemical Information and Modeling
  19. ClusPro in rounds 38 to 45 of CAPRI: Toward combining template‐based methods with free docking
    Dzmitry Padhorny, Kathryn A. Porter, Mikhail Ignatov, Andrey Evgen'evich Alekseenko, Dmitri Beglov, Sergei Kotelnikov, Ryota Ashizawa, Israel Desta, Nawsad Alam, Zhuyezi Sun et al. · 2020 · Proteins Structure Function and Bioinformatics
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  21. A memetic algorithm enables efficient local and global all-atom protein-protein docking with backbone and side-chain flexibility
    Daniel Varela, Vera Karlin, Ingemar André · 2022 · Structure
  22. Structural modeling of protein complexes: Current capabilities and challenges
    Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas · 2019 · Proteins Structure Function and Bioinformatics
  23. MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein–Protein Docking Conformations
    Yong Gyu Jung, Cunliang Geng, Alexandre M. J. J. Bonvin, Li C. Xue, Vasant Honavar · 2023 · Biomolecules
  24. A Web-Based Protocol for Interprotein Contact Prediction by Deep Learning
    Xiaoyang Jing, Hong Zeng, Sheng Wang, Jinbo Xu · 2019 · Methods in molecular biology
  25. Performance of human and server prediction in CAPRI rounds 38‐45
    Rui Duan, Liming Qiu, Xianjin Xu, Zhiwei Ma, Benjamin Ryan Merideth, Chi‐Ren Shyu, Xiaoqin Zou · 2020 · Proteins Structure Function and Bioinformatics
  26. Evaluation of CONSRANK-Like Scoring Functions for Rescoring Ensembles of Protein–Protein Docking Poses
    Guillaume Launay, Masahito Ohue, Julia Prieto Santero, Yuri Matsuzaki, Cécile Hilpert, Nobuyuki Uchikoga, Takanori Hayashi, Juliette Martin · 2020 · Frontiers in Molecular Biosciences
  27. Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained Docking
    Mateusz Zalewski, Sebastian Kmiecik, Michał Koliński · 2021 · Molecules
  28. Domain-Based Protein Docking with Extremely Large Conformational Changes
    Charles W. Christoffer, Daisuke Kihara · 2022 · Journal of Molecular Biology
  29. In silico prediction method for plant Nucleotide‐binding leucine‐rich repeat‐ and pathogen effector interactions
    Alicia Fick, Jacobus Lukas Marthinus Fick, Velushka Swart, Noëlani van den Berg · 2025 · The Plant Journal
  30. Modeling of protein complexes in CAPRI Round 37 using template‐based approach combined with model selection
    Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas · 2017 · Proteins Structure Function and Bioinformatics
  31. Allosteric Inhibition of Adenylyl Cyclase Type 5 by G-Protein: A Molecular Dynamics Study
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  32. Modeling protein–nucleic acid complexes with extremely large conformational changes using Flex‐LZerD
    Charles W. Christoffer, Daisuke Kihara · 2022 · PROTEOMICS
  33. Enhanced Molecular Dynamics Method to Efficiently Increase the Discrimination Capability of Computational Protein–Protein Docking
    Nicola Scafuri, Miguel Angel Soler, Andrea Spitaleri, Walter Rocchia · 2021 · Journal of Chemical Theory and Computation
  34. evERdock BAI: Machine-learning-guided selection of protein-protein complex structure
    Kei Terayama, Ai Shinobu, Koji Tsuda, Kazuhiro Takemura, Akio Kitao · 2019 · The Journal of Chemical Physics
  35. Protein–protein docking with interface residue restraints*
    Hao Li, Sheng‐You Huang · 2020 · Chinese Physics B
  36. Protein–Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations
    Mateusz Kurciński, Sebastian Kmiecik, Mateusz Zalewski, Andrzej Koliński · 2021 · International Journal of Molecular Sciences
  37. Achieving Accurate Standard Protein–Protein Binding Free Energy Calculations through the Geometrical Route and Ergodic Sampling
    Haohao Fu, Christophe J. Chipot, Xueguang Shao, Wensheng Cai · 2023 · Journal of Chemical Information and Modeling
  38. Development of a New Benchmark for Assessing the Scoring Functions Applicable to Protein–Protein Interactions
    Li Han, Qifan Yang, Zhihai Liu, Yan Li, Renxiao Wang · 2018 · Future Medicinal Chemistry
  39. Using yeast two-hybrid system and molecular dynamics simulation to detect venom protein-protein interactions
    Ying Jia, Paulina Kowalski, Ivan Lopez · 2021 · Current Research in Toxicology
  40. Challenges and Advantages of Accounting for Backbone Flexibility in Prediction of Protein–Protein Complexes
    Nabil F. Faruk, Xiangda Peng, Karl F. Freed, Benoı̂t Roux, Tobin R. Sosnick · 2022 · Journal of Chemical Theory and Computation
  41. Inclusion of Desolvation Energy into Protein–Protein Docking through Atomic Contact Potentials
    Hao Li, Yumeng Yan, Xuejun Zhao, Sheng‐You Huang · 2022 · Journal of Chemical Information and Modeling
  42. Bioinformatics and Chemometrics for Discovering Biologically Active Peptides From Food Proteins
    Kento Imai, Dawei Ji, Ifeanyi Daniel Nwachukwu, Dominic Agyei, Chibuike C. Udenigwe · 2019 · Elsevier eBooks
  43. Dockground Tool for Development and Benchmarking of Protein Docking Procedures
    Petras J. Kundrotas, Ian Kotthoff, Sherman W. Choi, Matthew M. Copeland, Ilya A. Vakser · 2020 · Methods in molecular biology
  44. AlphaFold models of host-pathogen interactions elucidate the prevalence and structural modes of molecular mimicry
    Delora Baptista, Lidia Gomez-Lucas, Jürgen Jänes, Nevan J. Krogan, Maria João Amorim, Ylva Ivarsson, Pedro Beltrão · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  45. Protein loops with multiple meta‐stable conformations: A challenge for sampling and scoring methods
    Amélie Barozet, Marc Bianciotto, Marc Vaisset, Thierry Siméon, Hervé Minoux, Juan Cortés · 2020 · Proteins Structure Function and Bioinformatics
  46. Design of Peptide Ligand for Lactoferrin and Study of Its Binding Specificity
    Tatiana M. Zimina, Nikita O. Sitkov, Vladimir Karasev, Yury А. Skorik, Alexey A. Kolobov, Alexander A. Kolobov, Nikolay S. Bunenkov, Viktor V. Luchinin · 2023 · Chemosensors
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  48. Predictive Modeling and Structure Analysis of Genetic Variants in Familial Hypercholesterolemia: Implications for Diagnosis and Protein Interaction Studies
    A. Larrea, Shifa Jebari‐Benslaiman, Unai Galicia García, Ane San Jose- Urteaga, Kepa B. Uribe, Asier Benito‐Vicente, César Martı́n · 2023 · Current Atherosclerosis Reports
  49. Determining Complex Structures using Docking Method with Single Particle Scattering Data
    Hongxiao Wang, Haiguang Liu · 2017 · Frontiers in Molecular Biosciences
  50. Residue interaction networks of K-Ras protein with water molecules identifies the potential role of switch II and P-loop
    S. Udhaya Kumar, C. George Priya Doss · 2021 · Computers in Biology and Medicine
  51. Biomolecular Interaction Prediction in the Pre‐ and Post‐ AlphaFold Era: The 8th CAPRI Evaluation
    Marc Ferdinand Lensink, Nessim RAOURAOUA, Guillaume Brysbaert, Sameer S Velankar, Shoshana J. Wodak, Alexandre M. J. J. Bonvin · 2025 · Proteins Structure Function and Bioinformatics
  52. Template-Based Modeling of Protein Complexes Using the PPI3D Web Server
    Justas Dapkūnas, Česlovas Venclovas · 2020 · Methods in molecular biology
  53. The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses
    Didier Barradas‐Bautista, Zhen Zhu Cao, Luigi Cavallo, Romina Oliva · 2020 · BMC Bioinformatics
  54. Computing the Dynamic Supramolecular Structural Proteome
    Ruth Nussinov, Jason A. Papin, Ilya A. Vakser · 2017 · PLoS Computational Biology
  55. iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machines
    Nicolas Renaud, Yong Gyu Jung, Vasant Honavar, Cunliang Geng, Alexandre M. J. J. Bonvin, Li C. Xue · 2020 · SoftwareX
  56. More efficient screening of protein-protein complex model structures for reducing the number of candidates
    Kazuhiro Takemura, Akio Kitao · 2019 · Biophysics and Physicobiology
  57. Computational characterization of the binding mode between oncoprotein Ets‐1 and DNA‐repair enzymes
    Jérôme de Ruyck, Guillaume Brysbaert, Vincent Villeret, Marc Aumercier, Marc Ferdinand Lensink · 2018 · Proteins Structure Function and Bioinformatics
  58. Template‐based modeling of diverse protein interactions in CAPRI rounds 38‐45
    Justas Dapkūnas, Visvaldas Kairys, Kliment Olechnovič, Česlovas Venclovas · 2019 · Proteins Structure Function and Bioinformatics
  59. Site‐Specific Studies of Nucleosome Interactions by Solid‐State NMR Spectroscopy
    ShengQi Xiang, Ulric B. le Paige, Velten Horn, Klaartje Houben, Marc Baldus, Hugo van Ingen · 2018 · Angewandte Chemie
  60. Docking, Scoring, and Virtual Screening in Drug Discovery
    Francesca Spyrakis, Aurijit Sarkar, Glen E. Kellogg · 2021 · Burger's Medicinal Chemistry and Drug Discovery
  61. Topological deep learning for enhancing peptide-protein complex prediction
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  62. Using Short Molecular Dynamics Simulations to Determine the Important Features of Interactions in Antibody–Protein Complexes
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  63. A Direct Role for the CD1b Endogenous Spacer in the Recognition of a Mycobacterium tuberculosis Antigen by T-Cell Receptors
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  64. Evaluation of potential MHC-I allele-specific epitopes in Zika virus proteins and the effects of mutations on peptide-MHC-I interaction studied using in silico approaches
    Aline Silva da Costa, Tácio Vinício Amorim Fernandes, Murilo Lamim Bello, Theo Luiz Ferraz de Souza · 2021 · Computational Biology and Chemistry
  65. De novo design of site-specific protein interactions with learned surface fingerprints
    Pablo Gaínza, Sarah Wehrle, Alexandra Van Hall‐Beauvais, Anthony Marchand, Andreas Scheck, Zander Harteveld, Stephen Buckley, Dongchun Ni, Shuguang Tan, Freyr Sverrisson et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  66. Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study
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  69. Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints
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  76. Protein-protein docking with large-scale backbone flexibility using coarse-grained Monte-Carlo simulations
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