Alexandre M. J. J. Bonvin

发表

Debora S. Marks, Thomas A. Hopf, Charlotta P. I. Schärfe, 2014 .

iSEE: Interface Structure, Evolution and Energy-based machine learning predictor of binding affinity changes upon mutations

Anna Vangone, Alexandre M. J. J. Bonvin, Cunliang Geng, 2018 .

Data-driven Docking: Using External Information to Spark the Biomolecular Rendez-vous

Alexandre M. J. J. Bonvin, Adrien S. J. Melquiond, 2010 .

Faculty Opinions recommendation of iPPI-DB: an online database of modulators of protein-protein interactions.

Alexandre M. J. J. Bonvin, 2015 .

Prediction of Biomolecular Complexes

Luigi Cavallo, Alexandre M. J. J. Bonvin, Anna Vangone, 2017 .

Computational Tools for the Structural Characterization of Proteins and Their Complexes from Sequence-Evolutionary Data

Irina S. Moreira, Alexandre M. J. J. Bonvin, Li C. Xue, 2018 .

Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK

João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin, Jorge Roel-Touris, 2019, Journal of chemical theory and computation.

Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK

João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin, C. G. Don, 2019, bioRxiv.

CASD-NMR: critical assessment of automated structure determination by NMR

Antonio Rosato, Michael Nilges, Paul Guerry, 2009, Nature Methods.

Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit

Alexandre M. J. J. Bonvin, Gydo C.P. van Zundert, A. Bonvin, 2015 .

Docking models for Docking Benchmark 4, 5 and CAPRI score_set

Alexandre M. J. J. Bonvin, Cunliang Geng, Li Xue, 2019 .

The GROMOS96 benchmarks for molecular simulation

Alexandre M. J. J. Bonvin, Wilfred F. van Gunsteren, Alan E. Mark, 2000 .

WeNMR: Structural Biology on the Grid

Dmitri I. Svergun, Stefano Dal Pra, Torsten Herrmann, 2011, Journal of Grid Computing.

Sharing Data from Molecular Simulations

Alexandre M. J. J. Bonvin, Helmut Grubmüller, Erik Lindahl, 2019, J. Chem. Inf. Model..

Faculty Opinions recommendation of Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies.

Alexandre M. J. J. Bonvin, A. Bonvin, 2016 .

West-Life: A Virtual Research Environment for structural biology

Andrea Giachetti, Chris Morris, Daniel Kouřil, 2019, Journal of structural biology: X.

MENSAdb: a thorough structural analysis of membrane protein dimers

Irina S. Moreira, Alexandre M. J. J. Bonvin, Pedro Matos-Filipe, 2019, Database J. Biol. Databases Curation.

Sequence co-evolution gives 3D contacts and structures of protein complexes

Debora S. Marks, Chris Sander, Thomas A. Hopf, 2014, bioRxiv.

A protein–DNA docking benchmark

Alexandre M. J. J. Bonvin, Marc van Dijk, A. Bonvin, 2008, Nucleic acids research.

A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking

Alexandre M. J. J. Bonvin, Adrien S. J. Melquiond, Mikael Trellet, 2013, PloS one.

Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?

Alexandre M. J. J. Bonvin, Cunliang Geng, Li C. Xue, 2019, WIREs Computational Molecular Science.

Combining NMR Relaxation with Chemical Shift Perturbation Data to Drive Protein–protein Docking

Alexandre M. J. J. Bonvin, Rolf Boelens, Robert Kaptein, 2006, Journal of biomolecular NMR.

Defining distance restraints in HADDOCK

João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin, Ezgi Karaca, 2018, Nature Protocols.

Protein–protein HADDocking using exclusively pseudocontact shifts

Alexandre M. J. J. Bonvin, Christophe Schmitz, 2011, Journal of biomolecular NMR.

Pushing the limits of what is achievable in protein–DNA docking: benchmarking HADDOCK’s performance

Alexandre M. J. J. Bonvin, Marc van Dijk, A. Bonvin, 2010, Nucleic acids research.

Solvated protein–DNA docking using HADDOCK

Alexandre M. J. J. Bonvin, Panagiotis L. Kastritis, P. Kastritis, 2013, Journal of Biomolecular NMR.

De and M.

Tsjerk A. Wassenaar, Alexandre M. J. J. Bonvin, Aurelien Thureau, 2007 .

Insight into cyanobacterial circadian timing from structural details of the KaiB–KaiC interaction

Alexandre M. J. J. Bonvin, Adrien S. J. Melquiond, Albert J. R. Heck, 2014, Proceedings of the National Academy of Sciences.

Understanding the Role of the Josephin Domain in the PolyUb Binding and Cleavage Properties of Ataxin-3

Giuseppe Nicastro, Alexandre M. J. J. Bonvin, Annalisa Pastore, 2010, PloS one.

Characterizing the N- and C-terminal Small Ubiquitin-like Modifier (SUMO)-interacting Motifs of the Scaffold Protein DAXX*

Alexandre M. J. J. Bonvin, Mark Okon, A. Bonvin, 2011, The Journal of Biological Chemistry.

Erratum: Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1 : HADDOCK in CASP-CAPRI Round 1 (Proteins: Structure, Function, and Bioinformatics, (2017), 85, 3, (417-423), 10.1002/prot.25198)

Anna Vangone, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin, 2017 .

CPORT: A Consensus Interface Predictor and Its Performance in Prediction-Driven Docking with HADDOCK

Alexandre M. J. J. Bonvin, Sjoerd J. de Vries, A. Bonvin, 2011, PloS one.