Sjoerd J. de Vries - Publications, H-index & Citations

Sjoerd J. de Vries

Utrecht University

24H指数

64论文数

7.0K被引数

收录论文 19

发表时间

SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking

FRONTIERS IN MOLECULAR BIOSCIENCES

IF4

2021-09-17

OAAI

Murail, Samuel; de Vries, Sjoerd J.; Rey, Julien; Moroy, Gautier; Tuffery, Pierre

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

NUCLEIC ACIDS RESEARCH

IF13.1

2019-05-22

OAAI

Karami, Yasaman; Rey, Julien; Postic, Guillaume; Murail, Samuel; Tuffery, Pierre; de Vries, Sjoerd J.

Fast and Accurate Grid Representations for Atom-Based Docking with Partner Flexibility

JOURNAL OF COMPUTATIONAL CHEMISTRY

IF4.8

2017-05-02

PREAI

de Vries, Sjoerd J.; Zacharias, Martin

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

NUCLEIC ACIDS RESEARCH

IF13.1

2017-04-29

OAAI

de Vries, Sjoerd J.; Rey, Julien; Schindler, Christina E. M.; Zacharias, Martin; Tuffery, Pierre

Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

IF2.8

2016-11-24

OAAI

Schindler, Christina E. M.; de Beauchene, Isaure Chauvot; de Vries, Sjoerd J.; Zacharias, Martin

Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins

NUCLEIC ACIDS RESEARCH

IF13.1

2016-04-29

OAAI

de Beauchene, Isaure Chauvot; de Vries, Sjoerd J.; Zacharias, Martin

Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling

BIOPHYSICAL JOURNAL

IF3.1

2016-02-01

OAAI

de Vries, Sjoerd J.; de Beauchene, Isaure Chauvot; Schindler, Christina E. M.; Zacharias, Martin

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

plos biology

IF3.6

2016-01-27

OAAI

de Beauchene, Isaure Chauvot; de Vries, Sjoerd J.; Zacharias, Martin

A Web Interface for Easy Flexible Protein-Protein Docking with ATTRACT

BIOPHYSICAL JOURNAL

IF3.1

2015-02-01

OAAI

de Vries, Sjoerd J.; Schindler, Christina E. M.; de Beauchene, Isaure Chauvot; Zacharias, Martin

iATTRACT: Simultaneous global and local interface optimization for protein-protein docking refinement

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

IF2.8

2014-12-18

PREAI

Schindler, Christina E. M.; de Vries, Sjoerd J.; Zacharias, Martin

Defining the limits of homology modeling in information-driven protein docking

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

IF2.8

2013-10-17

OAAI

Rodrigues, J. P. G. L. M.; Melquiond, A. S. J.; Karaca, E.; Trellet, M.; van Dijk, M.; van Zundert, G. C. P.; Schmitz, C.; de Vries, S. J.; Bordogna, A.; Bonati, L.; Kastritis, P. L.; Bonvin, Alexandre M. J. J.

WeNMR: Structural Biology on the Grid WeNMR: 网格上的结构生物学

JOURNAL OF GRID COMPUTING

IF2.9

2012-11-30

171

OAAI

Wassenaar, Tsjerk A.; van Dijk, Marc; Loureiro-Ferreira, Nuno; van der Schot, Gijs; de Vries, Sjoerd J.; Schmitz, Christophe; van der Zwan, Johan; Boelens, Rolf; Giachetti, Andrea; Ferella, Lucio; Rosato, Antonio; Bertini, Ivano; Herrmann, Torsten; Jonker, Hendrik R. A.; Bagaria, Anurag; Jaravine, Victor; Guntert, Peter; Schwalbe, Harald; Vranken, Wim F.; Doreleijers, Jurgen F.; Vriend, Gert; Vuister, Geerten W.; Franke, Daniel; Kikhney, Alexey; Svergun, Dmitri I.; Fogh, Rasmus H.; Ionides, John; Laue, Ernest D.; Spronk, Chris; Jurksa, Simonas; Verlato, Marco; Badoer, Simone; Dal Pra, Stefano; Mazzucato, Mirco; Frizziero, Eric; Bonvin, Alexandre M. J. J.

Building Macromolecular Assemblies by Information-driven Docking

MOLECULAR & CELLULAR PROTEOMICS

IF5.5

2010-08-01

113

OAAI

Karaca, Ezgi; Melquiond, Adrien S. J.; de Vries, Sjoerd J.; Kastritis, Panagiotis L.; Bonvin, Alexandre M. J. J.

Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

IF2.8

2010-07-06

OAAI

de Vries, Sjoerd J.; Melquiond, Adrien S. J.; Kastritis, Panagiotis L.; Karaca, Ezgi; Bordogna, Annalisa; van Dijk, Marc; Rodrigues, Joao P. G. L. M.; Bonvin, Alexandre M. J. J.

The HADDOCK web server for data-driven biomolecular docking

NATURE PROTOCOLS

IF16

2010-04-15

1.2K

OAAI

De Vries, Sjoerd J.; van Dijk, Marc; Bonvin, Alexandre M. J. J.

A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system (vol 5, art no. 295, 2009)

MOLECULAR SYSTEMS BIOLOGY

IF7.7

2009-10-13

OAAI

van Wijk, Sjoerd J. L.; de Vries, Sjoerd J.; Kemmeren, Patrick; Huang, Anding; Boelens, Rolf; Bonvin, Alexandre M. J. J.; Timmers, H. Th Marc

A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system

MOLECULAR SYSTEMS BIOLOGY

IF7.7

2009-08-18

138

OAAI

van Wijk, Sjoerd J. L.; de Vries, Sjoerd J.; Kemmeren, Patrick; Huang, Anding; Boelens, Rolf; Bonvin, Alexandre M. J. J.; Timmers, H. Th Marc

Data-driven homology modelling of P-glycoprotein in the ATP-bound state indicates flexibility of the transmembrane domains

FEBS JOURNAL

IF4.2

2009-01-23

OAAI

Stockner, Thomas; de Vries, Sjoerd J.; Bonvin, Alexandre M. J. J.; Ecker, Gerhard F.; Chiba, Peter

HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

IF2.8

2007-10-31

540

OAAI

De Vries, Sjoerd J.; van Dijk, Aalt D. J.; Krzeminski, Mickael; van Dijk, Mark; Thureau, Aurelien; Hsu, Victor; Wassenaar, Tsjerk; Bonvin, Alexandre M. J. J.

研究方向