Solvated docking: introducing water into the modelling of biomolecular complexes. - Aalt D. J. van Dijk; Alexandre M. J. J. Bonvin (Bioinform., 2006)

Intramolecular surface contacts contain information about protein-protein interface regions. - Sjoerd Jacob de Vries; Alexandre M. J. J. Bonvin (Bioinform., 2006)

3D-DART: a DNA structure modelling server. - Marc van Dijk; Alexandre M. J. J. Bonvin (Nucleic Acids Res., 2009)

SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes. - Mickaël Krzeminski; Karine Loth; Rolf Boelens; Alexandre M. J. J. Bonvin (BMC Bioinform., 2010)

WeNMR: Structural Biology on the Grid. - Tsjerk A. Wassenaar; Marc van Dijk; Nuno Loureiro-Ferreira; Gijs van der Schot; Sjoerd Jacob de Vries; Christophe Schmitz; Johan van der Zwan; Rolf Boelens; Andrea Giachetti 002; Lucio Ferella; Antonio Rosato; Ivano Bertini; et al. (IWSG-Life, 2011)

WeNMR: Structural Biology on the Grid. - Tsjerk A. Wassenaar; Marc van Dijk; Nuno Loureiro-Ferreira; Gijs van der Schot; Sjoerd Jacob de Vries; Christophe Schmitz; Johan van der Zwan; Rolf Boelens; Andrea Giachetti 002; Lucio Ferella; Antonio Rosato; Ivano Bertini; et al. (J. Grid Comput., 2012)

Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network. - Sjoerd J. L. van Wijk; Adrien S. J. Melquiond; Sjoerd Jacob de Vries; H. Th. Marc Timmers; Alexandre M. J. J. Bonvin (PLoS Comput. Biol., 2012)

HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein-Protein Interaction Inhibitors. - Panagiotis L. Kastritis; João P. G. L. M. Rodrigues; Alexandre M. J. J. Bonvin (J. Chem. Inf. Model., 2014)

DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes. - G. C. P. van Zundert; Alexandre M. J. J. Bonvin (Bioinform., 2015)

PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. - Li C. Xue; João P. G. L. M. Rodrigues; Panagiotis L. Kastritis; Alexandre M. J. J. Bonvin; Anna Vangone (Bioinform., 2016)

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 E. Mark (J. Chem. Inf. Model., 2016)

Template-based protein-protein docking exploiting pairwise interfacial residue restraints. - Li C. Xue; João P. G. L. M. Rodrigues; Drena Dobbs; Vasant G. Honavar; Alexandre M. J. J. Bonvin (Briefings Bioinform., 2017)

pdb-tools: a swiss army knife for molecular structures. - João P. G. L. M. Rodrigues; João M. C. Teixeira; Mikaël Trellet; Alexandre M. J. J. Bonvin (F1000Research, 2018)

Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. - Zeynep Kurkcuoglu; Panagiotis I. Koukos; Nevia Citro; Mikael E. Trellet; João P. G. L. M. Rodrigues; Irina S. Moreira; Jorge Roel-Touris; Adrien S. J. Melquiond; Cunliang Geng; Jörg Schaarschmidt; Li C. Xue; Anna Vangone; et al. (J. Comput. Aided Mol. Des., 2018)

PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes. - Brian Jiménez-García; Katarina Elez; Panagiotis I. Koukos; Alexandre M. J. J. Bonvin; Anna Vangone (Bioinform., 2019)

Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. - Anna Vangone; Jörg Schaarschmidt; Panagiotis I. Koukos; Cunliang Geng; Nevia Citro; Mikael E. Trellet; Li C. Xue; Alexandre M. J. J. Bonvin (Bioinform., 2019)

Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3. - Panagiotis I. Koukos; Li C. Xue; Alexandre M. J. J. Bonvin (J. Comput. Aided Mol. Des., 2019)

Sharing Data from Molecular Simulations. - Mark James Abraham; Rossen Apostolov; Jonathan Barnoud; Paul Bauer; Christian Blau; Alexandre M. J. J. Bonvin; Matthieu Chavent; John D. Chodera; Karmen Condic-Jurkic; Lucie Delemotte; Helmut Grubmüller; Rebecca J. Howard; et al. (J. Chem. Inf. Model., 2019)

Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape. - Andrea Basciu; Giuliano Malloci; Fabio Pietrucci; Alexandre M. J. J. Bonvin; Attilio Vittorio Vargiu (J. Chem. Inf. Model., 2019)

Computational approaches to therapeutic antibody design: established methods and emerging trends. - Richard A. Norman; Francesco Ambrosetti; Alexandre M. J. J. Bonvin; Lucy J. Colwell; Sebastian Kelm; Sandeep Kumar; Konrad Krawczyk (Briefings Bioinform., 2020)

proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking. - Francesco Ambrosetti; Tobias Hegelund Olsen; Pier Paolo Olimpieri; Brian Jiménez-García; Edoardo Milanetti; Paolo Marcatili; Alexandre M. J. J. Bonvin (Bioinform., 2020)

iScore: a novel graph kernel-based function for scoring protein-protein docking models. - Cunliang Geng; Yong Jung; Nicolas Renaud; Vasant G. Honavar; Alexandre M. J. J. Bonvin; Li C. Xue (Bioinform., 2020)

LightDock goes information-driven. - Jorge Roel-Touris; Alexandre M. J. J. Bonvin; Brian Jiménez-García (Bioinform., 2020)

Deep-learning enhancement of large scale numerical simulations. - Caspar van Leeuwen; Damian Podareanu; Valeriu Codreanu; Maxwell X. Cai; Axel Berg; Simon Portegies Zwart; Robin Stoffer; Menno Veerman; Chiel van Heerwaarden; Sydney Otten; Sascha Caron; Cunliang Geng; et al. (CoRR, 2020)

Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4. - Andrea Basciu; Panagiotis I. Koukos; Giuliano Malloci; Alexandre M. J. J. Bonvin; Attilio Vittorio Vargiu (J. Comput. Aided Mol. Des., 2020)

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 Jung; Vasant G. Honavar; Cunliang Geng; Alexandre M. J. J. Bonvin; Li C. Xue (SoftwareX, 2020)

MENSAdb: a thorough structural analysis of membrane protein dimers. - Pedro Matos-Filipe; António J. Preto; Panagiotis I. Koukos; Joana Mourão; Alexandre M. J. J. Bonvin; Irina S. Moreira (Database J. Biol. Databases Curation, 2021)

Structural biology in the clouds: The WeNMR-EOSC Ecosystem. - Rodrigo Vargas Honorato; Panagiotis I. Koukos; Brian Jiménez-García; Andrei Tsaregorodtsev; Marco Verlato; Andrea Giachetti 002; Antonio Rosato; Alexandre M. J. J. Bonvin (CoRR, 2021)

Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing. - Panagiotis I. Koukos; Manon Réau; Alexandre M. J. J. Bonvin (J. Chem. Inf. Model., 2021)

DeepRank-GNN: a graph neural network framework to learn patterns in protein-protein interfaces. - Manon Réau; Nicolas Renaud; Li C. Xue; Alexandre M. J. J. Bonvin (Bioinform., 2023)

Ranking protein-protein models with large language models and graph neural networks. - Xiaotong Xu; Alexandre M. J. J. Bonvin (CoRR, 2024)

Modeling Protein-Glycan Interactions with HADDOCK. - Anna Ranaudo; Marco Giulini; Angela Pelissou Ayuso; Alexandre M. J. J. Bonvin (J. Chem. Inf. Model., 2024)

Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins. - Andrea Basciu; Mohd Athar; Han Kurt; Christine Neville; Giuliano Malloci; Fabrizio C. Muredda; Andrea Bosin; Paolo Ruggerone; Alexandre M. J. J. Bonvin; Attilio Vittorio Vargiu (J. Chem. Inf. Model., 2025)

HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes. - Marco Giulini; Victor Reys; João M. C. Teixeira; Brian Jiménez-García; Rodrigo V. Honorato; Anna Kravchenko; Xiaotong Xu; Raphaëlle Versini; Anna Engel; Stefan Verhoeven; Alexandre M. J. J. Bonvin (J. Chem. Inf. Model., 2025)