Alexandre M. J. J. Bonvin

35 papers Journal 34Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes.
J. Chem. Inf. Model.
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
2025 J jnl
Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins.
J. Chem. Inf. Model.
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
2024 J jnl
Modeling Protein-Glycan Interactions with HADDOCK.
J. Chem. Inf. Model.
Anna Ranaudo, Marco Giulini, Angela Pelissou Ayuso, Alexandre M. J. J. Bonvin
2024 J jnl
Ranking protein-protein models with large language models and graph neural networks.
CoRR
Xiaotong Xu, Alexandre M. J. J. Bonvin
2024 J jnl
Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven docking.
Bioinform.
Marco Giulini, Constantin Schneider, Daniel Cutting, Nikita Desai, Charlotte M. Deane, Alexandre M. J. J. Bonvin
2023 J jnl
DeepRank-GNN: a graph neural network framework to learn patterns in protein-protein interfaces.
Bioinform.
Manon Réau, Nicolas Renaud, Li C. Xue, Alexandre M. J. J. Bonvin
2021 J jnl
MENSAdb: a thorough structural analysis of membrane protein dimers.
Database J. Biol. Databases Curation
Pedro Matos-Filipe, António J. Preto, Panagiotis I. Koukos, Joana Mourão, Alexandre M. J. J. Bonvin, Irina S. Moreira
2021 J jnl
Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing.
J. Chem. Inf. Model.
Panagiotis I. Koukos, Manon Réau, Alexandre M. J. J. Bonvin
2021 J jnl
Structural biology in the clouds: The WeNMR-EOSC Ecosystem.
CoRR
Rodrigo Vargas Honorato, Panagiotis I. Koukos, Brian Jiménez-García, Andrei Tsaregorodtsev, Marco Verlato, Andrea Giachetti, Antonio Rosato, Alexandre M. J. J. Bonvin
2020 J jnl
Computational approaches to therapeutic antibody design: established methods and emerging trends.
Briefings Bioinform.
Richard A. Norman, Francesco Ambrosetti, Alexandre M. J. J. Bonvin, Lucy J. Colwell, Sebastian Kelm, Sandeep Kumar, Konrad Krawczyk
2020 J jnl
Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4.
J. Comput. Aided Mol. Des.
Andrea Basciu, Panagiotis I. Koukos, Giuliano Malloci, Alexandre M. J. J. Bonvin, Attilio Vittorio Vargiu
2020 J jnl
Deep-learning enhancement of large scale numerical simulations.
CoRR
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, Francesco Ambrosetti, Alexandre M. J. J. Bonvin
2020 J jnl
LightDock goes information-driven.
Bioinform.
Jorge Roel-Touris, Alexandre M. J. J. Bonvin, Brian Jiménez-García
2020 J jnl
iScore: An MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines.
SoftwareX
Nicolas Renaud, Yong Jung, Vasant G. Honavar, Cunliang Geng, Alexandre M. J. J. Bonvin, Li C. Xue
2020 J jnl
iScore: a novel graph kernel-based function for scoring protein-protein docking models.
Bioinform.
Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant G. Honavar, Alexandre M. J. J. Bonvin, Li C. Xue
2020 J jnl
proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking.
Bioinform.
Francesco Ambrosetti, Tobias Hegelund Olsen, Pier Paolo Olimpieri, Brian Jiménez-García, Edoardo Milanetti, Paolo Marcatili, Alexandre M. J. J. Bonvin
2019 J jnl
Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape.
J. Chem. Inf. Model.
Andrea Basciu, Giuliano Malloci, Fabio Pietrucci, Alexandre M. J. J. Bonvin, Attilio Vittorio Vargiu
2019 J jnl
Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server.
Bioinform.
Anna Vangone, Jörg Schaarschmidt, Panagiotis I. Koukos, Cunliang Geng, Nevia Citro, Mikael E. Trellet, Li C. Xue, Alexandre M. J. J. Bonvin
2019 J jnl
PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes.
Bioinform.
Brian Jiménez-García, Katarina Elez, Panagiotis I. Koukos, Alexandre M. J. J. Bonvin, Anna Vangone
2019 J jnl
Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3.
J. Comput. Aided Mol. Des.
Panagiotis I. Koukos, Li C. Xue, Alexandre M. J. J. Bonvin
2019 J jnl
Sharing Data from Molecular Simulations.
J. Chem. Inf. Model.
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, E. Joseph Jordan, Erik Lindahl, Samuli Ollila, Jana Selent, Daniel G. A. Smith, Phillip J. Stansfeld, Johanna K. S. Tiemann, Mikaël Trellet, Christopher J. Woods, Artem A. Zhmurov
2018 J jnl
Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2.
J. Comput. Aided Mol. Des.
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, Alexandre M. J. J. Bonvin
2018 J jnl
pdb-tools: a swiss army knife for molecular structures.
F1000Research
João P. G. L. M. Rodrigues, João M. C. Teixeira, Mikaël Trellet, Alexandre M. J. J. Bonvin
2017 J jnl
Template-based protein-protein docking exploiting pairwise interfacial residue restraints.
Briefings Bioinform.
Li C. Xue, João P. G. L. M. Rodrigues, Drena Dobbs, Vasant G. Honavar, Alexandre M. J. J. Bonvin
2016 J jnl
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.
J. Chem. Inf. Model.
Evelyne Deplazes, Josephine Davies, Alexandre M. J. J. Bonvin, Glenn F. King, Alan E. Mark
2016 J jnl
PRODIGY: a web server for predicting the binding affinity of protein-protein complexes.
Bioinform.
Li C. Xue, João P. G. L. M. Rodrigues, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin, Anna Vangone
2015 J jnl
DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes.
Bioinform.
G. C. P. van Zundert, Alexandre M. J. J. Bonvin
2014 J jnl
HADDOCK
J. Chem. Inf. Model.
Panagiotis L. Kastritis, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin
2012 J jnl
Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network.
PLoS Comput. Biol.
Sjoerd J. L. van Wijk, Adrien S. J. Melquiond, Sjoerd Jacob de Vries, H. Th. Marc Timmers, Alexandre M. J. J. Bonvin
2012 J jnl
WeNMR: Structural Biology on the Grid.
J. Grid Comput.
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, Lucio Ferella, Antonio Rosato, Ivano Bertini, Torsten Herrmann, Hendrik R. A. Jonker, Anurag Bagaria, Victor Jaravine, Peter Güntert, Harald Schwalbe, Wim F. Vranken, Jurgen F. Doreleijers, Gert Vriend, Geerten W. Vuister, Daniel Franke, Alexey Kikhney, Dmitri I. Svergun, Rasmus H. Fogh, John M. C. Ionides, Ernest D. Laue, Chris A. E. M. Spronk, Simonas Jurksa, Marco Verlato, Simone Badoer, Stefano Dal Pra, Mirco Mazzucato, Eric Frizziero, Alexandre M. J. J. Bonvin
2011 — conf
WeNMR: Structural Biology on the Grid.
IWSG-Life
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, Lucio Ferella, Antonio Rosato, Ivano Bertini, Torsten Herrmann, Hendrik R. A. Jonker, Anurag Bagaria, Victor Jaravine, Peter Güntert, Harald Schwalbe, Wim F. Vranken, Jurgen F. Doreleijers, Gert Vriend, Geerten W. Vuister, Daniel Franke, Alexey Kikhney, Dmitri I. Svergun, Rasmus H. Fogh, John M. C. Ionides, Ernest D. Laue, Chris A. E. M. Spronk, Marco Verlato, Simone Badoer, Stefano Dal Pra, Mirco Mazzucato, Eric Frizziero, Alexandre M. J. J. Bonvin
2010 J jnl
SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes.
BMC Bioinform.
Mickaël Krzeminski, Karine Loth, Rolf Boelens, Alexandre M. J. J. Bonvin
2009 J jnl
3D-DART: a DNA structure modelling server.
Nucleic Acids Res.
Marc van Dijk, Alexandre M. J. J. Bonvin
2006 J jnl
Intramolecular surface contacts contain information about protein-protein interface regions.
Bioinform.
Sjoerd Jacob de Vries, Alexandre M. J. J. Bonvin
2006 J jnl
Solvated docking: introducing water into the modelling of biomolecular complexes.
Bioinform.
Aalt D. J. van Dijk, Alexandre M. J. J. Bonvin