Publications by authors named "Sjoerd de Vries"

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Breast cancer survival prediction using an automated mitosis detection pipeline.
Nikolas Stathonikos, Marc Aubreville, Sjoerd de Vries, Frauke Wilm, Christof A Bertram

J Pathol Clin Res· November 2024

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Don't be misled: 3 misconceptions about external validation of clinical prediction models.
Hannah M la Roi-Teeuw, Florien S van Royen, Anne de Hond, Anum Zahra, Sjoerd de Vries

J Clin Epidemiol· August 2024

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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 Beauchene

BMC Bioinformatics· March 2024

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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, Sjoerd de Vries

J Chem Inf Model· October 2023

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PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution.
Julien Rey, Samuel Murail, Sjoerd de Vries, Philippe Derreumaux, Pierre Tuffery

Nucleic Acids Res· July 2023

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ProtNAff: protein-bound Nucleic Acid filters and fragment libraries.
Antoine Moniot, Yann Guermeur, Sjoerd Jacob de Vries, Isaure Chauvot de Beauchene

Bioinformatics· August 2022

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A semi-supervised decision support system to facilitate antibiotic stewardship for urinary tract infections.
Sjoerd de Vries, Thijs Ten Doesschate, Joan E E Totté, Judith W Heutz, Yvette G T Loeffen

Comput Biol Med· July 2022

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SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking.
Samuel Murail, Sjoerd J de Vries, Julien Rey, Gautier Moroy, Pierre Tufféry

Front Mol Biosci· September 2021

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Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach.
Glenn Glashagen, Sjoerd de Vries, Urszula Uciechowska-Kaczmarzyk, Sergey A Samsonov, Samuel Murail

Proteins· August 2020

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The search of sequence variants using a constrained protein evolution simulation approach.
Pierre Tufféry, Sjoerd de Vries

Comput Struct Biotechnol J· June 2020

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DaReUS-Loop: a web server to model multiple loops in homology models.
Yasaman Karami, Julien Rey, Guillaume Postic, Samuel Murail, Pierre Tufféry, Sjoerd J de Vries

Nucleic Acids Res· July 2019

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Higher-level cognitive functions in Dutch elite and sub-elite table tennis players.
Marije T Elferink-Gemser, Irene R Faber, Chris Visscher, Tsung-Min Hung, Sjoerd J de Vries

PLoS One· April 2019

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DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins.
Yasaman Karami, Frédéric Guyon, Sjoerd De Vries, Pierre Tufféry

Sci Rep· September 2018

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Investigating the reliability and validity of the Dutch versions of the illness management and recovery scales among clients with mental disorders.
Peter J J Goossens, Titus A A Beentjes, Suzanne Knol, Michelle P Salyers, Sjoerd J de Vries

J Ment Health· December 2017

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Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking.
Alexander Sasse, Sjoerd J de Vries, Christina E M Schindler, Isaure Chauvot de Beauchêne, Martin Zacharias

PLoS One· August 2017

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The pepATTRACT web server for blind, large-scale peptide-protein docking.
Sjoerd J de Vries, Julien Rey, Christina E M Schindler, Martin Zacharias, Pierre Tuffery

Nucleic Acids Res· July 2017

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Fast and accurate grid representations for atom-based docking with partner flexibility.
Sjoerd J de Vries, Martin Zacharias

J Comput Chem· June 2017

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Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI.
Christina E M Schindler, Isaure Chauvot de Beauchêne, Sjoerd J de Vries, Martin Zacharias

Proteins· March 2017

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SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes.
Christina E M Schindler, Sjoerd J de Vries, Alexander Sasse, Martin Zacharias

Structure· August 2016

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Recovery of motor imagery ability in the first year after stroke.
Wya Feenstra, Marga Tepper, Anne M Boonstra, Bert Otten, Sjoerd de Vries

Int J Rehabil Res· June 2016

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Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins.
Isaure Chauvot de Beauchene, Sjoerd J de Vries, Martin Zacharias

Nucleic Acids Res· June 2016

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Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling.
Sjoerd J de Vries, Isaure Chauvot de Beauchêne, Christina E M Schindler, Martin Zacharias

Biophys J· February 2016

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Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach.
Isaure Chauvot de Beauchene, Sjoerd J de Vries, Martin Zacharias

PLoS Comput Biol· January 2016

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Fully Blind Peptide-Protein Docking with pepATTRACT.
Christina E M Schindler, Sjoerd J de Vries, Martin Zacharias

Structure· August 2015

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A web interface for easy flexible protein-protein docking with ATTRACT.
Sjoerd J de Vries, Christina E M Schindler, Isaure Chauvot de Beauchêne, Martin Zacharias

Biophys J· February 2015

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