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ORCIDSjoerd Jacob de Vries
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2020 – today
- 2024
[j11]Anna Kravchenko, Sjoerd Jacob de Vries, Malika Smaïl-Tabbone, Isaure Chauvot de Beauchêne:
HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses. BMC Bioinform. 25(1): 129 (2024)- 2023
- [j10]Yasaman Karami
, Samuel Murail, Julien Giribaldi, Benjamin Lefranc, Florian Defontaine, Olivier Lesouhaitier, Jérôme Leprince, Sjoerd Jacob de Vries, Pierre Tufféry:
Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization. J. Chem. Inf. Model. 63(20): 6436-6450 (2023) - [j9]Julien Rey, Samuel Murail, Sjoerd Jacob de Vries, Philippe Derreumaux, Pierre Tufféry:
PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution. Nucleic Acids Res. 51(W1): 432-437 (2023) - 2022
- [j8]Antoine Moniot, Yann Guermeur, Sjoerd Jacob de Vries, Isaure Chauvot de Beauchêne:
ProtNAff: protein-bound Nucleic Acid filters and fragment libraries. Bioinform. 38(16): 3911-3917 (2022)
2010 – 2019
- 2019
- [j7]Yasaman Karami, Julien Rey, Guillaume Postic, Samuel Murail, Pierre Tufféry, Sjoerd Jacob de Vries:
DaReUS-Loop: a web server to model multiple loops in homology models. Nucleic Acids Res. 47(Webserver-Issue): W423-W428 (2019) - 2017
- [j6]Sjoerd Jacob de Vries, Martin Zacharias:
Fast and accurate grid representations for atom-based docking with partner flexibility. J. Comput. Chem. 38(17): 1538-1546 (2017) - [j5]Sjoerd Jacob 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): W361-W364 (2017) - 2016
- [j4]Isaure Chauvot de Beauchêne, Sjoerd Jacob 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) - 2012
- [j3]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:
WeNMR: Structural Biology on the Grid. J. Grid Comput. 10(4): 743-767 (2012) - [j2]Sjoerd J. L. van Wijk, Adrien S. J. Melquiond, Sjoerd Jacob 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) - 2011
- [c1]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:
WeNMR: Structural Biology on the Grid. IWSG-Life 2011
2000 – 2009
- 2006
- [j1]Sjoerd Jacob de Vries, Alexandre M. J. J. Bonvin:
Intramolecular surface contacts contain information about protein-protein interface regions. Bioinform. 22(17): 2094-2098 (2006)
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