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
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
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
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
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
Contacts-based prediction of binding affinity in protein–protein complexes
A Vangone, AMJJ Bonvin
eLife 4, e07454, 2015
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
Flexible protein-protein docking
AMJJ Bonvin
Current opinion in structural biology 16 (2), 194-200, 2006
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
3D-DART: a DNA structure modelling server
M Van Dijk, AMJJ Bonvin
Nucleic acids research 37 (suppl 2), W235-W239, 2009
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
A structure‐based benchmark for protein–protein binding affinity
PL Kastritis, IH Moal, H Hwang, Z Weng, PA Bates, AMJJ Bonvin, J Janin
Protein Science 20 (3), 482-491, 2011
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