A
Alexandre M. J. J. Bonvin
Researcher at Utrecht University
Publications - 338
Citations - 25898
Alexandre M. J. J. Bonvin is an academic researcher from Utrecht University. The author has contributed to research in topics: Docking (molecular) & Protein structure. The author has an hindex of 70, co-authored 322 publications receiving 21694 citations. Previous affiliations of Alexandre M. J. J. Bonvin include ETH Zurich & University of Lausanne.
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HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.
TL;DR: An approach called HADDOCK (High Ambiguity Driven protein-protein Docking) that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments or mutagenesis data to drive the docking process.
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The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.
G. C. P. van Zundert,João P. G. L. M. Rodrigues,Mikael Trellet,Christophe Schmitz,Panagiotis L. Kastritis,Ezgi Karaca,Adrien S. J. Melquiond,M. van Dijk,S.J. de Vries,Alexandre M. J. J. Bonvin +9 more
TL;DR: The updated version 2.2.2 of the HADDOCK portal is presented, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface.
Journal ArticleDOI
The HADDOCK web server for data-driven biomolecular docking
TL;DR: The HADDOCK web server protocol is presented, facilitating the modeling of biomolecular complexes for a wide community, and has access to the resources of a dedicated cluster and of the e-NMR GRID infrastructure.
Journal ArticleDOI
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 +4 more
TL;DR: Protein binDIng enerGY prediction (PRODIGY), a web server to predict the binding affinity of protein-protein complexes from their 3D structure based on intermolecular contacts and properties derived from non-interface surface is presented.
Journal ArticleDOI
Refinement of protein structures in explicit solvent.
Jens P. Linge,Mark A. Williams,Christian A.E.M. Spronk,Alexandre M. J. J. Bonvin,Michael Nilges +4 more
TL;DR: The results demonstrate the significant improvement of structure quality by a short refinement in a thin layer of solvent and show that a dihedral angle energy term in the force field is beneficial for structure calculation and refinement.