Alexandre M.J.J. Bonvin
Alexandre M.J.J. Bonvin
Professor of Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of
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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
23552003
The HADDOCK web server for data-driven biomolecular docking
SJ De Vries, M Van Dijk, AMJJ Bonvin
Nature protocols 5 (5), 883-897, 2010
9982010
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
6602016
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
6342003
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
5922007
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
5192004
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
4892004
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
4112010
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
3712007
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
3702006
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
3262005
Flexible protein-protein docking
AMJJ Bonvin
Current opinion in structural biology 16 (2), 194-200, 2006
3232006
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
3062014
3D-DART: a DNA structure modelling server
M Van Dijk, AMJJ Bonvin
Nucleic acids research 37 (suppl 2), W235-W239, 2009
2872009
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
2762013
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
2172011
Are Scoring Functions in Protein− Protein Docking Ready to Predict Interactomes? Clues from a Novel Binding Affinity Benchmark
PL Kastritis, AMJJ Bonvin
J. Proteome Res 10 (2), 921-922, 2011
2132011
Are Scoring Functions in Protein− Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark
PL Kastritis, AMJJ Bonvin
Journal of proteome research 9 (5), 2216-2225, 2010
2132010
Data‐driven docking for the study of biomolecular complexes
ADJ Van Dijk, R Boelens, AMJJ Bonvin
The FEBS journal 272 (2), 293-312, 2005
1922005
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
1822015
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