Alexandre M.J.J. Bonvin
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HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
C Dominguez, R Boelens, AMJJ Bonvin
Journal of the American Chemical Society 125 (7), 1731-1737, 2003
The HADDOCK2. 2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes
GCP van Zundert, J Rodrigues, M Trellet, C Schmitz, PL Kastritis, ...
Journal of molecular biology 428 (4), 720-725, 2016
The HADDOCK web server for data-driven biomolecular docking
SJ De Vries, M Van Dijk, AMJJ Bonvin
Nature protocols 5 (5), 883-897, 2010
PRODIGY: a web server for predicting the binding affinity of protein–protein complexes
LC Xue, JP Rodrigues, PL Kastritis, AM Bonvin, A Vangone
Bioinformatics 32 (23), 3676-3678, 2016
Refinement of protein structures in explicit solvent
JP Linge, MA Williams, CAEM Spronk, AMJJ Bonvin, M Nilges
Proteins: Structure, Function, and Bioinformatics 50 (3), 496-506, 2003
HADDOCK versus HADDOCK: new features and performance of HADDOCK2. 0 on the CAPRI targets
SJ de Vries, ADJ van Dijk, M Krzeminski, M van Dijk, A Thureau, V Hsu, ...
Proteins: structure, function, and bioinformatics 69 (4), 726-733, 2007
The nisin–lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics
STD Hsu, E Breukink, E Tischenko, MAG Lutters, B De Kruijff, R Kaptein, ...
Nature structural & molecular biology 11 (10), 963-967, 2004
Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes
CG Kalodimos, N Biris, AMJJ Bonvin, MM Levandoski, M Guennuegues, ...
Science 305 (5682), 386-389, 2004
Plectasin, a fungal defensin, targets the bacterial cell wall precursor Lipid II
T Schneider, T Kruse, R Wimmer, I Wiedemann, V Sass, U Pag, A Jansen, ...
Science 328 (5982), 1168-1172, 2010
On the binding affinity of macromolecular interactions: daring to ask why proteins interact
PL Kastritis, AMJJ Bonvin
Journal of The Royal Society Interface 10 (79), 20120835, 2013
Sequence co-evolution gives 3D contacts and structures of protein complexes
TA Hopf, CPI Schärfe, JP Rodrigues, AG Green, O Kohlbacher, C Sander, ...
Elife 3, e03430, 2014
The α‐to‐β conformational transition of Alzheimer's Aβ‐(1–42) peptide in aqueous media is reversible: a step by step conformational analysis suggests the location of β …
S Tomaselli, V Esposito, P Vangone, NAJ van Nuland, AMJJ Bonvin, ...
ChemBioChem 7 (2), 257-267, 2006
Contacts-based prediction of binding affinity in protein–protein complexes
A Vangone, AMJJ Bonvin
eLife 4, e07454, 2015
Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR
I Gelis, AMJJ Bonvin, D Keramisanou, M Koukaki, G Gouridis, ...
Cell 131 (4), 756-769, 2007
Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2
T Vreven, IH Moal, A Vangone, BG Pierce, PL Kastritis, M Torchala, ...
Journal of molecular biology 427 (19), 3031-3041, 2015
Structural biology in the clouds: the WeNMR-EOSC ecosystem
RV Honorato, PI Koukos, B Jiménez-García, A Tsaregorodtsev, M Verlato, ...
Frontiers in Molecular Biosciences 8, 729513, 2021
Flexible protein-protein docking
AMJJ Bonvin
Current opinion in structural biology 16 (2), 194-200, 2006
3D-DART: a DNA structure modelling server
M Van Dijk, AMJJ Bonvin
Nucleic acids research 37 (suppl 2), W235-W239, 2009
RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
AJ Nederveen, JF Doreleijers, W Vranken, Z Miller, CAEM Spronk, ...
PROTEINS: Structure, Function, and Bioinformatics 59 (4), 662-672, 2005
CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK
SJ de Vries, AMJJ Bonvin
PLoS One 6 (3), e17695, 2011
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