Intramolecular surface contacts contain information about protein-protein interface regions. - Sjoerd Jacob de Vries; Alexandre M. J. J. Bonvin (Bioinform., 2006)

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 002; Lucio Ferella; Antonio Rosato; Ivano Bertini; et al. (IWSG-Life, 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 002; Lucio Ferella; Antonio Rosato; Ivano Bertini; et al. (J. Grid Comput., 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)

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)

Fast and accurate grid representations for atom-based docking with partner flexibility. - Sjoerd Jacob de Vries; Martin Zacharias (J. Comput. Chem., 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)

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)

ProtNAff: protein-bound Nucleic Acid filters and fragment libraries. - Antoine Moniot; Yann Guermeur; Sjoerd Jacob de Vries; Isaure Chauvot de Beauchêne (Bioinform., 2022)

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., 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., 2023)

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., 2024)