Sjoerd J. de Vries

Publication Activity (10 Years)

Years Active: 2006-2019
Publications (10 Years): 4

Top Topics

Protein Sequences

Mass Spectrometry

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

J. Comput. Chem.

J. Grid Comput.

Publications

Yasaman Karami, Julien Rey, Guillaume Postic, Samuel Murail, Pierre Tufféry, Sjoerd J. de Vries
DaReUS-Loop: a web server to model multiple loops in homology models. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Sjoerd J. de Vries, Martin Zacharias
Fast and accurate grid representations for atom-based docking with partner flexibility. J. Comput. Chem. 38 (17) (2017)
Sjoerd J. de Vries, Julien Rey, Christina E. M. Schindler, Martin Zacharias, Pierre Tufféry
The pepATTRACT web server for blind, large-scale peptide-protein docking. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Isaure Chauvot de Beauchêne, Sjoerd J. de Vries, Martin Zacharias
Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach. PLoS Comput. Biol. 12 (1) (2016)
Tsjerk A. Wassenaar, Marc van Dijk, Nuno Loureiro-Ferreira, Gijs van der Schot, Sjoerd J. de Vries, Christophe Schmitz, Johan van der Zwan, Rolf Boelens, Andrea Giachetti, Lucio Ferella, Antonio Rosato, Ivano Bertini, Torsten Herrmann, Hendrik R. A. Jonker, Anurag Bagaria, Victor Jaravine, Peter Güntert, Harald Schwalbe, Wim F. Vranken, Jurgen F. Doreleijers, Gert Vriend, Geerten W. Vuister, Daniel Franke, Alexey Kikhney, Dmitri I. Svergun, Rasmus H. Fogh, John M. C. Ionides, Ernest D. Laue, Chris A. E. M. Spronk, Simonas Jurksa, Marco Verlato, Simone Badoer, Stefano Dal Pra, Mirco Mazzucato, Eric Frizziero, Alexandre M. J. J. Bonvin
WeNMR: Structural Biology on the Grid. J. Grid Comput. 10 (4) (2012)
Sjoerd J. L. van Wijk, Adrien S. J. Melquiond, Sjoerd J. de Vries, H. Th. Marc Timmers, Alexandre M. J. J. Bonvin
Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network. PLoS Comput. Biol. 8 (11) (2012)
Tsjerk A. Wassenaar, Marc van Dijk, Nuno Loureiro-Ferreira, Gijs van der Schot, Sjoerd J. de Vries, Christophe Schmitz, Johan van der Zwan, Rolf Boelens, Andrea Giachetti, Lucio Ferella, Antonio Rosato, Ivano Bertini, Torsten Herrmann, Hendrik R. A. Jonker, Anurag Bagaria, Victor Jaravine, Peter Güntert, Harald Schwalbe, Wim F. Vranken, Jurgen F. Doreleijers, Gert Vriend, Geerten W. Vuister, Daniel Franke, Alexey Kikhney, Dmitri I. Svergun, Rasmus H. Fogh, John M. C. Ionides, Ernest D. Laue, Chris A. E. M. Spronk, Marco Verlato, Simone Badoer, Stefano Dal Pra, Mirco Mazzucato, Eric Frizziero, Alexandre M. J. J. Bonvin
WeNMR: Structural Biology on the Grid. IWSG-Life (2011)
Sjoerd J. de Vries, Alexandre M. J. J. Bonvin
Intramolecular surface contacts contain information about protein-protein interface regions. Bioinform. 22 (17) (2006)