Alexandre M. J. J. Bonvin

According to our database1, Alexandre M. J. J. Bonvin authored at least 28 papers between 2006 and 2021.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 


Online presence:



Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing.
J. Chem. Inf. Model., 2021

Structural biology in the clouds: The WeNMR-EOSC Ecosystem.
CoRR, 2021

MENSAdb: a thorough structural analysis of membrane protein dimers.
Database J. Biol. Databases Curation, 2021

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

Deep-learning enhancement of large scale numerical simulations.
CoRR, 2020

LightDock goes information-driven.
Bioinform., 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

Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape.
J. Chem. Inf. Model., 2019

Sharing Data from Molecular Simulations.
J. Chem. Inf. Model., 2019

Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3.
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

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

Template-based protein-protein docking exploiting pairwise interfacial residue restraints.
Briefings Bioinform., 2017

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

DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes.
Bioinform., 2015

HADDOCK<sub>2P2I</sub>: A Biophysical Model for Predicting the Binding Affinity of Protein-Protein Interaction Inhibitors.
J. Chem. Inf. Model., 2014

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

WeNMR: Structural Biology on the Grid.
J. Grid Comput., 2012


SAMPLEX: Automatic mapping of perturbed and unperturbed regions of proteins and complexes.
BMC Bioinform., 2010

3D-DART: a DNA structure modelling server.
Nucleic Acids Res., 2009

Intramolecular surface contacts contain information about protein-protein interface regions.
Bioinform., 2006

Solvated docking: introducing water into the modelling of biomolecular complexes.
Bioinform., 2006