Gert Vriend

51 papers Journal 47Unranked 4
YearRankTypeTitle / Venue / Authors
2018 J jnl
A Critical Note on Symmetry Contact Artifacts and the Evaluation of the Quality of Homology Models.
Symmetry
Dipali Singh, Karen R. M. Berntsen, Coos Baakman, Gert Vriend, Tapobrata Lahiri
2018 J jnl
Bio-knowledge-based filters improve residue-residue contact prediction accuracy.
Bioinform.
Pawel P. Wozniak, J. Pelc, M. Skrzypecki, Gert Vriend, Malgorzata Kotulska
2017 J jnl
Correlated mutations select misfolded from properly folded proteins.
Bioinform.
Pawel P. Wozniak, Gert Vriend, Malgorzata Kotulska
2017 J jnl
Forecasting residue-residue contact prediction accuracy.
Bioinform.
Pawel P. Wozniak, Bogumil Konopka, J. Xu, Gert Vriend, Malgorzata Kotulska
2017 J jnl
Molden 2.0: quantum chemistry meets proteins.
J. Comput. Aided Mol. Des.
Gijs Schaftenaar, Elias Vlieg, Gert Vriend
2016 J jnl
GPCRdb: an information system for G protein-coupled receptors.
Nucleic Acids Res.
Vignir Ísberg, Stefan Mordalski, Christian Munk, Krzysztof Rataj, Kasper Harpsøe, Alexander S. Hauser, Bas Vroling, Andrzej J. Bojarski, Gert Vriend, David E. Gloriam
2016 J jnl
KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins.
Bioinform.
Joanna Lange, Lucjan Stanislaw Wyrwicz, Gert Vriend
2016 J jnl
Tools and data services registry: a community effort to document bioinformatics resources.
Nucleic Acids Res.
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. Jiménez, 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
2016 J jnl
iPPI-DB: an online database of modulators of protein-protein interactions.
Nucleic Acids Res.
Céline M. Labbé, Mélaine A. Kuenemann, Barbara Zarzycka, Gert Vriend, Gerry A. F. Nicolaes, David Lagorce, Maria A. Miteva, Bruno O. Villoutreix, Olivier Sperandio
2015 J jnl
A series of PDB-related databanks for everyday needs.
Nucleic Acids Res.
Wouter G. Touw, Coos Baakman, Jon Black, Tim A. H. te Beek, Elmar Krieger, Robbie P. Joosten, Gert Vriend
2015 — conf
Blind and Visually Impaired Students Can Perform Computer-Aided Molecular Design with an Assistive Molecular Fabricator.
IWBBIO (1)
Valère Lounnas, Henry B. Wedler, Timothy Newman, Jon Black, Gert Vriend
2015 J jnl
Discovery of Small Molecule CD40-TRAF6 Inhibitors.
J. Chem. Inf. Model.
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
2015 J jnl
New ways to boost molecular dynamics simulations.
J. Comput. Chem.
Elmar Krieger, Gert Vriend
2014 J jnl
GPCRDB: an information system for G protein-coupled receptors.
Nucleic Acids Res.
Vignir Ísberg, Bas Vroling, Rob van der Kant, Kang Li, Gert Vriend, David E. Gloriam
2014 — conf
The NewProt Self-Service Portal for Protein Engineering.
SWAT4LS
Andreas Schwarte, Hanka Venselaar, Peter Haase, Gert Vriend
2014 J jnl
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.
Valère Lounnas, Henry B. Wedler, Timothy Newman, Gijs Schaftenaar, Jason G. Harrison, Gabriella Nepomuceno, Ryan Pemberton, Dean J. Tantillo, Gert Vriend
2014 J jnl
YASARA View - molecular graphics for all devices - from smartphones to workstations.
Bioinform.
Elmar Krieger, Gert Vriend
2013 J jnl
Status quo of annotation of human disease variants.
BMC Bioinform.
Hanka Venselaar, Franscesca Camilli, Shima Gholizadeh, Marlou Snelleman, Han G. Brunner, Gert Vriend
2012 J jnl
AsteriX: A Web Server To Automatically Extract Ligand Coordinates from Figures in PDF Articles.
J. Chem. Inf. Model.
Valère Lounnas, Gert Vriend
2012 J jnl
Drug design for ever, from hype to hope.
J. Comput. Aided Mol. Des.
G. Seddon, Valère Lounnas, Ross McGuire, T. van den Bergh, Robert P. Bywater, Laerte Oliveira, Gert Vriend
2012 J jnl
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.
Nucleic Acids Res.
Jurgen F. Doreleijers, Wim F. Vranken, Christopher F. Schulte, John L. Markley, Eldon L. Ulrich, Gert Vriend, Geerten W. Vuister
2012 J jnl
NucleaRDB: information system for nuclear receptors.
Nucleic Acids Res.
Bas Vroling, David Thorne, Philip McDermott, Henk-Jan Joosten, Teresa K. Attwood, Steve Pettifer, Gert Vriend
2012 J jnl
WeNMR: Structural Biology on the Grid.
J. Grid Comput.
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, 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
2011 J jnl
A series of PDB related databases for everyday needs.
Nucleic Acids Res.
Robbie P. Joosten, Tim A. H. te Beek, Elmar Krieger, Maarten L. Hekkelman, Rob W. W. Hooft, Reinhard Schneider, Chris Sander, Gert Vriend
2011 J jnl
Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank.
Bioinform.
Robbie P. Joosten, Krista Joosten, Serge X. Cohen, Gert Vriend, Anastassis Perrakis
2011 J jnl
GPCRDB: information system for G protein-coupled receptors.
Nucleic Acids Res.
Bas Vroling, Marijn P. A. Sanders, Coos Baakman, Annika Borrmann, Stefan Verhoeven, Jan P. G. Klomp, Laerte Oliveira, Jacob de Vlieg, Gert Vriend
2011 J jnl
Integrating GPCR-specific information with full text articles.
BMC Bioinform.
Bas Vroling, David Thorne, Philip McDermott, Teresa K. Attwood, Gert Vriend, Steve Pettifer
2011 — conf
WeNMR: Structural Biology on the Grid.
IWSG-Life
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, 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
2010 J jnl
Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces.
BMC Bioinform.
Hanka Venselaar, Tim A. H. te Beek, Remko K. P. Kuipers, Maarten L. Hekkelman, Gert Vriend
2010 J jnl
The EMBRACE web service collection.
Nucleic Acids Res.
Steve Pettifer, Jon C. Ison, Matús Kalas, Dave Thorne, Philip McDermott, Inge Jonassen, Ali Liaquat, José María Fernández, José 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
2010 J jnl
WIWS: a protein structure bioinformatics Web service collection.
Nucleic Acids Res.
Maarten L. Hekkelman, Tim A. H. te Beek, Steve Pettifer, David Thorne, Terri K. Attwood, Gert Vriend
2009 J jnl
An active registry for bioinformatics web services.
Bioinform.
Steve Pettifer, David Thorne, Philip McDermott, Terri K. Attwood, J. Baran, Jan Christian Bryne, Taavi Hupponen, D. Mowbray, Gert Vriend
2008 J jnl
3D-Fun: predicting enzyme function from structure.
Nucleic Acids Res.
Marcin von Grotthuss, Dariusz Plewczynski, Gert Vriend, Leszek Rychlewski
2008 J jnl
Tracing evolutionary pressure.
Bioinform.
Kai Ye, Gert Vriend, Adriaan P. IJzerman
2006 J jnl
Correcting ligands, metabolites, and pathways.
BMC Bioinform.
Martin A. Ott, Gert Vriend
2006 J jnl
Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors.
PLoS Comput. Biol.
Sander B. Nabuurs, Chris A. E. M. Spronk, Geerten W. Vuister, Gert Vriend
2005 J jnl
GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases.
Nucleic Acids Res.
Marc A. van Driel, K. Cuelenaere, P. P. C. W. Kemmeren, Jack A. M. Leunissen, Han G. Brunner, Gert Vriend
2005 J jnl
MRS: a fast and compact retrieval system for biological data.
Nucleic Acids Res.
Maarten L. Hekkelman, Gert Vriend
2004 — conf
Invited Talk: Information Flux Through Proteins.
German Conference on Bioinformatics
Gert Vriend
2003 J jnl
Batch mode generation of residue-based diagrams of proteins.
Bioinform.
Fabien Campagne, Emmanuel Bettler, Gert Vriend, Harel Weinstein
2003 J jnl
NRMD: Nuclear Receptor Mutation Database.
Nucleic Acids Res.
Joost J. J. van Durme, Emmanuel Bettler, Simon Folkertsma, Florence Horn, Gert Vriend
2003 J jnl
NRSAS: Nuclear Receptor Structure Analysis Servers.
Nucleic Acids Res.
Emmanuel Bettler, Roland Krause, Florence Horn, Gert Vriend
2002 J jnl
Models@Home: distributed computing in bioinformatics using a screensaver based approach.
Bioinform.
Elmar Krieger, Gert Vriend
2001 J jnl
A sequence and structural study of transmembrane helices.
J. Comput. Aided Mol. Des.
Robert P. Bywater, David Thomas, Gert Vriend
1998 J jnl
GPCRDB: an information system for G protein-coupled receptors.
Nucleic Acids Res.
Florence Horn, Jonathan Weare, Margot W. Beukers, S. Hörsch, Amos Bairoch, W. Chen, Øyvind Edvardsen, Fabien Campagne, Gert Vriend
1998 J jnl
Homology modeling, model and software evaluation: three related resources.
Bioinform.
Rolando Rodríguez, Glay Chinea, Nelia Lopez, Tirso Pons, Gert Vriend
1997 J jnl
Objectively judging the quality of a protein structure from a Ramachandran plot.
Comput. Appl. Biosci.
Rob W. W. Hooft, Chris Sander, Gert Vriend
1996 J jnl
PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules.
J. Comput. Aided Mol. Des.
Daan M. F. van Aalten, Robert P. Bywater, John B. C. Findlay, Manfred Hendlich, Rob W. W. Hooft, Gert Vriend
1996 J jnl
The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value.
Comput. Appl. Biosci.
Rob W. W. Hooft, Chris Sander, Michael Scharf, Gert Vriend
1993 J jnl
A common motif in G-protein-coupled seven transmembrane helix receptors.
J. Comput. Aided Mol. Des.
Laerte Oliveira, A. C. M. Paiva, Gert Vriend
1993 J jnl
Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases.
J. Comput. Aided Mol. Des.
Gert Vriend, Vincent Eijsink