Gert Vriend

Publication Activity (10 Years)

Years Active: 1993-2018
Publications (10 Years): 9

Top Topics

Protein Interaction

Sequence Alignment

Top Venues

Nucleic Acids Res.

J. Comput. Aided Mol. Des.

J. Chem. Inf. Model.

Publications

Pawel P. Wozniak, J. Pelc, M. Skrzypecki, Gert Vriend, Malgorzata Kotulska
Bio-knowledge-based filters improve residue-residue contact prediction accuracy. Bioinform. 34 (21) (2018)
Dipali Singh, Karen R. M. Berntsen, Coos Baakman, Gert Vriend, Tapobrata Lahiri
A Critical Note on Symmetry Contact Artifacts and the Evaluation of the Quality of Homology Models. Symmetry 10 (1) (2018)
Gijs Schaftenaar, Elias Vlieg, Gert Vriend
Molden 2.0: quantum chemistry meets proteins. J. Comput. Aided Mol. Des. 31 (9) (2017)
Pawel P. Wozniak, Gert Vriend, Malgorzata Kotulska
Correlated mutations select misfolded from properly folded proteins. Bioinform. 33 (10) (2017)
Pawel P. Wozniak, Bogumil Konopka, J. Xu, Gert Vriend, Malgorzata Kotulska
Forecasting residue-residue contact prediction accuracy. Bioinform. 33 (21) (2017)
Céline M. Labbé, Mélaine A. Kuenemann, Barbara Zarzycka, Gert Vriend, Gerry A. F. Nicolaes, David Lagorce, Maria A. Miteva, Bruno O. Villoutreix, Olivier Sperandio
iPPI-DB: an online database of modulators of protein-protein interactions. Nucleic Acids Res. 44 (Database-Issue) (2016)
Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jimenez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44 (Database-Issue) (2016)
Vignir Ísberg, Stefan Mordalski, Christian Munk, Krzysztof Rataj, Kasper Harpsøe, Alexander S. Hauser, Bas Vroling, Andrzej J. Bojarski, Gert Vriend, David E. Gloriam
GPCRdb: an information system for G protein-coupled receptors. Nucleic Acids Res. 44 (Database-Issue) (2016)
Joanna Lange, Lucjan Stanislaw Wyrwicz, Gert Vriend
KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins. Bioinform. 32 (6) (2016)
Barbara Zarzycka, Tom Seijkens, Sander B. Nabuurs, Tina Ritschel, Jochen Grommes, Oliver Soehnlein, Roy Schrijver, Claudia M. van Tiel, Tilman M. Hackeng, Christian Weber, Fabian Giehler, Arnd Kieser, Esther Lutgens, Gert Vriend, Gerry A. F. Nicolaes
Discovery of Small Molecule CD40-TRAF6 Inhibitors. J. Chem. Inf. Model. 55 (2) (2015)
Elmar Krieger, Gert Vriend
New ways to boost molecular dynamics simulations. J. Comput. Chem. 36 (13) (2015)
Wouter G. Touw, Coos Baakman, Jon Black, Tim A. H. te Beek, Elmar Krieger, Robbie P. Joosten, Gert Vriend
A series of PDB-related databanks for everyday needs. Nucleic Acids Res. 43 (Database-Issue) (2015)
Valère Lounnas, Henry B. Wedler, Timothy Newman, Jon Black, Gert Vriend
Blind and Visually Impaired Students Can Perform Computer-Aided Molecular Design with an Assistive Molecular Fabricator. IWBBIO (1) (2015)
Valère Lounnas, Henry B. Wedler, Timothy Newman, Gijs Schaftenaar, Jason G. Harrison, Gabriella Nepomuceno, Ryan Pemberton, Dean J. Tantillo, Gert Vriend
Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol. J. Comput. Aided Mol. Des. 28 (11) (2014)
Vignir Ísberg, Bas Vroling, Rob van der Kant, Kang Li, Gert Vriend, David E. Gloriam
GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res. 42 (Database-Issue) (2014)
Elmar Krieger, Gert Vriend
YASARA View - molecular graphics for all devices - from smartphones to workstations. Bioinform. 30 (20) (2014)
Andreas Schwarte, Hanka Venselaar, Peter Haase, Gert Vriend
The NewProt Self-Service Portal for Protein Engineering. SWAT4LS (2014)
Hanka Venselaar, Franscesca Camilli, Shima Gholizadeh, Marlou Snelleman, Han G. Brunner, Gert Vriend
Status quo of annotation of human disease variants. BMC Bioinform. 14 (2013)
Jurgen F. Doreleijers, Wim F. Vranken, Christopher F. Schulte, John L. Markley, Eldon L. Ulrich, Gert Vriend, Geerten W. Vuister
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. Nucleic Acids Res. 40 (Database-Issue) (2012)
Tsjerk A. Wassenaar, Marc van Dijk, Nuno Loureiro-Ferreira, Gijs van der Schot, Sjoerd J. 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) (2012)
G. Seddon, Valère Lounnas, Ross McGuire, T. van den Bergh, Robert P. Bywater, Laerte Oliveira, Gert Vriend
Drug design for ever, from hype to hope. J. Comput. Aided Mol. Des. 26 (1) (2012)
Valère Lounnas, Gert Vriend
AsteriX: A Web Server To Automatically Extract Ligand Coordinates from Figures in PDF Articles. J. Chem. Inf. Model. 52 (2) (2012)
Bas Vroling, David Thorne, Philip McDermott, Henk-Jan Joosten, Teresa K. Attwood, Steve Pettifer, Gert Vriend
NucleaRDB: information system for nuclear receptors. Nucleic Acids Res. 40 (Database-Issue) (2012)
Robbie P. Joosten, Tim A. H. te Beek, Elmar Krieger, Maarten L. Hekkelman, Rob W. W. Hooft, Reinhard Schneider, Chris Sander, Gert Vriend
A series of PDB related databases for everyday needs. Nucleic Acids Res. 39 (Database-Issue) (2011)
Robbie P. Joosten, Krista Joosten, Serge X. Cohen, Gert Vriend, Anastassis Perrakis
Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank. Bioinform. 27 (24) (2011)
Bas Vroling, Marijn P. A. Sanders, Coos Baakman, Annika Borrmann, Stefan Verhoeven, Jan P. G. Klomp, Laerte Oliveira, Jacob de Vlieg, Gert Vriend
GPCRDB: information system for G protein-coupled receptors. Nucleic Acids Res. 39 (Database-Issue) (2011)
Tsjerk A. Wassenaar, Marc van Dijk, Nuno Loureiro-Ferreira, Gijs van der Schot, Sjoerd J. 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)
Bas Vroling, David Thorne, Philip McDermott, Teresa K. Attwood, Gert Vriend, Steve Pettifer
Integrating GPCR-specific information with full text articles. BMC Bioinform. 12 (2011)
Maarten L. Hekkelman, Tim A. H. te Beek, Steve Pettifer, David Thorne, Terri K. Attwood, Gert Vriend
WIWS: a protein structure bioinformatics Web service collection. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Steve Pettifer, Jon C. Ison, Matús Kalas, Dave Thorne, Philip McDermott, Inge Jonassen, Ali Liaquat, José María Fernández, Jose Manuel Rodriguez, David G. Pisano, Christophe Blanchet, Mahmut Uludag, Peter M. Rice, Edita Bartaseviciute, Kristoffer Rapacki, Maarten L. Hekkelman, Olivier Sand, Heinz Stockinger, Andrew B. Clegg, Erik Bongcam-Rudloff, Jean Salzemann, Vincent Breton, Teresa K. Attwood, Graham Cameron, Gert Vriend
The EMBRACE web service collection. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Hanka Venselaar, Tim A. H. te Beek, Remko K. P. Kuipers, Maarten L. Hekkelman, Gert Vriend
Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinform. 11 (2010)
Steve Pettifer, David Thorne, Philip McDermott, Terri K. Attwood, J. Baran, Jan Christian Bryne, Taavi Hupponen, D. Mowbray, Gert Vriend
An active registry for bioinformatics web services. Bioinform. 25 (16) (2009)
Kai Ye, Gert Vriend, Adriaan P. IJzerman
Tracing evolutionary pressure. Bioinform. 24 (7) (2008)
Marcin von Grotthuss, Dariusz Plewczynski, Gert Vriend, Leszek Rychlewski
3D-Fun: predicting enzyme function from structure. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Martin A. Ott, Gert Vriend
Correcting ligands, metabolites, and pathways. BMC Bioinform. 7 (2006)
Sander B. Nabuurs, Chris A. E. M. Spronk, Geerten W. Vuister, Gert Vriend
Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors. PLoS Comput. Biol. 2 (2) (2006)
Marc A. van Driel, K. Cuelenaere, P. P. C. W. Kemmeren, Jack A. M. Leunissen, Han G. Brunner, Gert Vriend
GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Maarten L. Hekkelman, Gert Vriend
MRS: a fast and compact retrieval system for biological data. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Gert Vriend
Invited Talk: Information Flux Through Proteins. German Conference on Bioinformatics (2004)
Fabien Campagne, Emmanuel Bettler, Gert Vriend, Harel Weinstein
Batch mode generation of residue-based diagrams of proteins. Bioinform. 19 (14) (2003)
Joost J. J. van Durme, Emmanuel Bettler, Simon Folkertsma, Florence Horn, Gert Vriend
NRMD: Nuclear Receptor Mutation Database. Nucleic Acids Res. 31 (1) (2003)
Emmanuel Bettler, Roland Krause, Florence Horn, Gert Vriend
NRSAS: Nuclear Receptor Structure Analysis Servers. Nucleic Acids Res. 31 (13) (2003)
Elmar Krieger, Gert Vriend
Models@Home: distributed computing in bioinformatics using a screensaver based approach. Bioinform. 18 (2) (2002)
Robert P. Bywater, David Thomas, Gert Vriend
A sequence and structural study of transmembrane helices. J. Comput. Aided Mol. Des. 15 (6) (2001)
Florence Horn, Jonathan Weare, Margot W. Beukers, S. Hörsch, Amos Bairoch, W. Chen, Øyvind Edvardsen, Fabien Campagne, Gert Vriend
GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res. 26 (1) (1998)
R. Rodríguez, G. Chinea, N. Lopez, Tirso Pons, Gert Vriend
Homology modeling, model and software evaluation: three related resources. Bioinform. 14 (6) (1998)
Rob W. W. Hooft, Chris Sander, Gert Vriend
Objectively judging the quality of a protein structure from a Ramachandran plot. Comput. Appl. Biosci. 13 (4) (1997)
Rob W. W. Hooft, Chris Sander, Michael Scharf, Gert Vriend
The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. Comput. Appl. Biosci. 12 (6) (1996)
Daan M. F. van Aalten, Robert P. Bywater, John B. C. Findlay, Manfred Hendlich, Rob W. W. Hooft, Gert Vriend
PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J. Comput. Aided Mol. Des. 10 (3) (1996)
Laerte Oliveira, A. C. M. Paiva, Gert Vriend
A common motif in G-protein-coupled seven transmembrane helix receptors. J. Comput. Aided Mol. Des. 7 (6) (1993)
Gert Vriend, Vincent Eijsink
Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases. J. Comput. Aided Mol. Des. 7 (4) (1993)