Sjoerd Jacob de Vries

12 papers Journal 11Unranked 1

Year	Rank	Type	Title / Venue / Authors
2024	J	`jnl`	HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses. BMC Bioinform. Anna Kravchenko, Sjoerd Jacob de Vries, Malika Smaïl-Tabbone, Isaure Chauvot de Beauchêne
2023	J	`jnl`	Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization. J. Chem. Inf. Model. Yasaman Karami, Samuel Murail, Julien Giribaldi, Benjamin Lefranc, Florian Defontaine, Olivier Lesouhaitier, Jérôme Leprince, Sjoerd Jacob de Vries, Pierre Tufféry
2023	J	`jnl`	PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution. Nucleic Acids Res. Julien Rey, Samuel Murail, Sjoerd Jacob de Vries, Philippe Derreumaux, Pierre Tufféry
2022	J	`jnl`	ProtNAff: protein-bound Nucleic Acid filters and fragment libraries. Bioinform. Antoine Moniot, Yann Guermeur, Sjoerd Jacob de Vries, Isaure Chauvot de Beauchêne
2019	J	`jnl`	DaReUS-Loop: a web server to model multiple loops in homology models. Nucleic Acids Res. Yasaman Karami, Julien Rey, Guillaume Postic, Samuel Murail, Pierre Tufféry, Sjoerd Jacob de Vries
2017	J	`jnl`	Fast and accurate grid representations for atom-based docking with partner flexibility. J. Comput. Chem. Sjoerd Jacob de Vries, Martin Zacharias
2017	J	`jnl`	The pepATTRACT web server for blind, large-scale peptide-protein docking. Nucleic Acids Res. Sjoerd Jacob de Vries, Julien Rey, Christina E. M. Schindler, Martin Zacharias, Pierre Tufféry
2016	J	`jnl`	Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach. PLoS Comput. Biol. Isaure Chauvot de Beauchêne, Sjoerd Jacob de Vries, Martin Zacharias
2012	J	`jnl`	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. Sjoerd J. L. van Wijk, Adrien S. J. Melquiond, Sjoerd Jacob de Vries, H. Th. Marc Timmers, Alexandre M. J. J. Bonvin
2012	J	`jnl`	WeNMR: Structural Biology on the Grid. J. Grid Comput. 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
2011	—	`conf`	WeNMR: Structural Biology on the Grid. IWSG-Life 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
2006	J	`jnl`	Intramolecular surface contacts contain information about protein-protein interface regions. Bioinform. Sjoerd Jacob de Vries, Alexandre M. J. J. Bonvin