Alexandre M. J. J. Bonvin
Orcid: 0000-0001-7369-1322
According to our database1,
Alexandre M. J. J. Bonvin
authored at least 34 papers
between 2006 and 2025.
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Bibliography
2025
HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes.
J. Chem. Inf. Model., 2025
Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins.
J. Chem. Inf. Model., 2025
2024
CoRR, 2024
2023
DeepRank-GNN: a graph neural network framework to learn patterns in protein-protein interfaces.
Bioinform., January, 2023
2021
Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing.
J. Chem. Inf. Model., 2021
Database J. Biol. Databases Curation, 2021
2020
iScore: An MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines.
SoftwareX, 2020
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., 2020
iScore: a novel graph kernel-based function for scoring protein-protein docking models.
Bioinform., 2020
proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking.
Bioinform., 2020
Computational approaches to therapeutic antibody design: established methods and emerging trends.
Briefings Bioinform., 2020
2019
Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape.
J. Chem. Inf. Model., 2019
J. Comput. Aided Mol. Des., 2019
Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server.
Bioinform., 2019
PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes.
Bioinform., 2019
2018
Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2.
J. Comput. Aided Mol. Des., 2018
2017
Template-based protein-protein docking exploiting pairwise interfacial residue restraints.
Briefings Bioinform., 2017
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.
J. Chem. Inf. Model., 2016
PRODIGY: a web server for predicting the binding affinity of protein-protein complexes.
Bioinform., 2016
2015
DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes.
Bioinform., 2015
2014
HADDOCK<sub>2P2I</sub>: A Biophysical Model for Predicting the Binding Affinity of Protein-Protein Interaction Inhibitors.
J. Chem. Inf. Model., 2014
2012
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., 2012
2011
Proceedings of the 3rd International Workshop on Science Gateways for Life Sciences, 2011
2010
SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes.
BMC Bioinform., 2010
2009
2006
Intramolecular surface contacts contain information about protein-protein interface regions.
Bioinform., 2006
Bioinform., 2006