Sjoerd Jacob de Vries

According to our database, Sjoerd Jacob de Vries authored at least 12 papers between 2006 and 2024.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2024

HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses.

Anna Kravchenko, Sjoerd Jacob de Vries, Malika Smaïl-Tabbone, Isaure Chauvot de Beauchêne

BMC Bioinform., December, 2024

2023

Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization.

Yasaman Karami, Samuel Murail, Julien Giribaldi, Benjamin Lefranc, Florian Defontaine, Olivier Lesouhaitier, Jérôme Leprince, Sjoerd Jacob de Vries, Pierre Tufféry

J. Chem. Inf. Model., October, 2023

PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution.

Julien Rey, Samuel Murail, Sjoerd Jacob de Vries, Philippe Derreumaux, Pierre Tufféry

Nucleic Acids Res., July, 2023

2022

ProtNAff: protein-bound Nucleic Acid filters and fragment libraries.

Antoine Moniot, Yann Guermeur, Sjoerd Jacob de Vries, Isaure Chauvot de Beauchêne

Bioinform., 2022

2019

DaReUS-Loop: a web server to model multiple loops in homology models.

Yasaman Karami, Julien Rey, Guillaume Postic, Samuel Murail, Pierre Tufféry, Sjoerd Jacob de Vries

Nucleic Acids Res., 2019

2017

The pepATTRACT web server for blind, large-scale peptide-protein docking.

Sjoerd Jacob de Vries, Julien Rey, Christina E. M. Schindler, Martin Zacharias, Pierre Tufféry

Nucleic Acids Res., 2017

Fast and accurate grid representations for atom-based docking with partner flexibility.

Sjoerd Jacob de Vries, Martin Zacharias

J. Comput. Chem., 2017

2016

Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach.

Isaure Chauvot de Beauchêne, Sjoerd Jacob de Vries, Martin Zacharias

PLoS Comput. Biol., 2016

2012

Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network.

Sjoerd J. L. van Wijk, Adrien S. J. Melquiond, Sjoerd Jacob de Vries, H. Th. Marc Timmers, Alexandre M. J. J. Bonvin

PLoS Comput. Biol., 2012

WeNMR: Structural Biology on the Grid.

Tsjerk A. Wassenaar, Marc van Dijk, Nuno Loureiro-Ferreira, Gijs van der Schot, Sjoerd Jacob 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

J. Grid Comput., 2012

2011

WeNMR: Structural Biology on the Grid.

Tsjerk A. Wassenaar, Marc van Dijk, Nuno Loureiro-Ferreira, Gijs van der Schot, Sjoerd Jacob 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

Proceedings of the 3rd International Workshop on Science Gateways for Life Sciences, 2011

2006

Intramolecular surface contacts contain information about protein-protein interface regions.

Sjoerd Jacob de Vries, Alexandre M. J. J. Bonvin

Bioinform., 2006