Sjoerd de Vries
Sjoerd de Vries
Research Engineer, CMPLI, Paris
Geverifieerd e-mailadres voor inserm.fr
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The HADDOCK web server for data-driven biomolecular docking
SJ De Vries, M Van Dijk, AMJJ Bonvin
Nature protocols 5 (5), 883, 2010
10102010
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
6942016
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
5942007
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
1852011
A comprehensive framework of E2–RING E3 interactions of the human ubiquitin–proteasome system
SJL Van Wijk, SJ De Vries, P Kemmeren, A Huang, R Boelens, ...
Molecular systems biology 5 (1), 295, 2009
1632009
WHISCY: what information does surface conservation yield? Application to data‐driven docking
SJ de Vries, ADJ van Dijk, AMJJ Bonvin
Proteins: Structure, Function, and Bioinformatics 63 (3), 479-489, 2006
1622006
WeNMR: structural biology on the grid
TA Wassenaar, M Van Dijk, N Loureiro-Ferreira, G Van Der Schot, ...
Journal of Grid Computing 10 (4), 743-767, 2012
1592012
How proteins get in touch: interface prediction in the study of biomolecular complexes
SJ de Vries, AMJJ Bonvin
Current protein and peptide science 9 (4), 394-406, 2008
1212008
Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server
E Karaca, ASJ Melquiond, SJ De Vries, PL Kastritis, AMJJ Bonvin
Molecular & Cellular Proteomics 9 (8), 1784-1794, 2010
1192010
Data‐driven docking: HADDOCK's adventures in CAPRI
ADJ Van Dijk, SJ De Vries, C Dominguez, H Chen, HX Zhou, A Bonvin
Proteins: Structure, Function, and Bioinformatics 60 (2), 232-238, 2005
1032005
Blind testing of routine, fully automated determination of protein structures from NMR data
A Rosato, JM Aramini, C Arrowsmith, A Bagaria, D Baker, A Cavalli, ...
Structure 20 (2), 227-236, 2012
762012
Fully blind peptide-protein docking with pepATTRACT
CEM Schindler, SJ de Vries, M Zacharias
Structure 23 (8), 1507-1515, 2015
682015
A web interface for easy flexible protein-protein docking with ATTRACT
SJ de Vries, CEM Schindler, IC de Beauchźne, M Zacharias
Biophysical journal 108 (3), 462-465, 2015
552015
Defining the limits of homology modeling in information‐driven protein docking
J Rodrigues, ASJ Melquiond, E Karaca, M Trellet, M Van Dijk, ...
Proteins: Structure, Function, and Bioinformatics 81 (12), 2119-2128, 2013
502013
Strengths and weaknesses of data‐driven docking in critical assessment of prediction of interactions
SJ de Vries, ASJ Melquiond, PL Kastritis, E Karaca, A Bordogna, ...
Proteins: Structure, Function, and Bioinformatics 78 (15), 3242-3249, 2010
452010
Data‐driven homology modelling of P‐glycoprotein in the ATP‐bound state indicates flexibility of the transmembrane domains
T Stockner, SJ de Vries, AMJJ Bonvin, GF Ecker, P Chiba
The FEBS journal 276 (4), 964-972, 2009
452009
iATTRACT: Simultaneous global and local interface optimization for protein–protein docking refinement
CEM Schindler, SJ de Vries, M Zacharias
Proteins: Structure, Function, and Bioinformatics 83 (2), 248-258, 2015
412015
Chauvot de Beauchene I, Zacharias M. A web interface for easy flexible protein-protein docking with ATTRACT
SJ De Vries, CE Schindler
Biophys. J 108 (3), 462-465, 2015
412015
ATTRACT-EM: a new method for the computational assembly of large molecular machines using cryo-EM maps
SJ de Vries, M Zacharias
PLOS one 7 (12), e49733, 2012
402012
Flexible docking and refinement with a coarse‐grained protein model using ATTRACT
S de Vries, M Zacharias
Proteins: Structure, Function, and Bioinformatics 81 (12), 2167-2174, 2013
382013
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Artikelen 1–20