G
Gerrit Vriend
Researcher at European Bioinformatics Institute
Publications - 78
Citations - 6230
Gerrit Vriend is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: Thermolysin & Thermostability. The author has an hindex of 38, co-authored 78 publications receiving 5948 citations. Previous affiliations of Gerrit Vriend include University of Groningen.
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PredictProtein—an open resource for online prediction of protein structural and functional features
Guy Yachdav,Edda Kloppmann,László Kaján,Maximilian Hecht,Tatyana Goldberg,Tobias Hamp,Peter Hönigschmid,Andrea Schafferhans,Manfred Roos,Michael Bernhofer,Lothar Richter,Haim Ashkenazy,Marco Punta,Avner Schlessinger,Yana Bromberg,Reinhard Schneider,Gerrit Vriend,Chris Sander,Nir Ben-Tal,Burkhard Rost +19 more
TL;DR: The goal has always been to develop a system optimized to meet the demands of experimentalists not highly experienced in bioinformatics, and the PredictProtein results are presented as both text and a series of intuitive, interactive and visually appealing figures.
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New POU dimer configuration mediates antagonistic control of an osteopontin preimplantation enhancer by Oct-4 and Sox-2.
Valérie Botquin,Heike Hess,Guy Fuhrmann,Constantinos Anastassiadis,Michael K. Gross,Gerrit Vriend,Hans R. Schöler +6 more
TL;DR: The POU transcription factor Oct-4 is expressed specifically in the germ line, pluripotent cells of the pregastrulation embryo and stem cell lines derived from the early embryo.
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Quality control of protein models : directional atomic contact analysis
Gerrit Vriend,Chris Sander +1 more
TL;DR: In this article, a contact quality index is defined as a measure of the agreement between the distributions of atoms around each residue fragment in the model and equivalent distributions derived from the database of known structures solved at high resolution.
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Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures.
TL;DR: A method is presented that positions polar hydrogen atoms in protein structures by optimizing the total hydrogen bond energy by using an empirical hydrogen bond force field derived from small molecule crystal structures.
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Prediction of Protein Conformational Freedom From Distance Constraints
B. L. de Groot,D.M.F. van Aalten,Ruud M. Scheek,Andrea Amadei,Gerrit Vriend,Herman J. C. Berendsen +5 more
TL;DR: Applications to an IgG‐binding domain, an SH3 binding domain, HPr, calmodulin, and lysozyme are presented which illustrate the use of the method as a fast and simple way to predict structural variability in proteins.