Gert Vriend

According to our database, Gert Vriend authored at least 60 papers between 1993 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2021

PredictProtein - Predicting Protein Structure and Function for 29 Years.

Michael Bernhofer, Christian Dallago, Timothy Karl, Venkata P. Satagopam, Michael Heinzinger, Maria Littmann, Tobias Olenyi, Jiajun Qiu, Konstantin Schütze, Guy Yachdav, Haim Ashkenazy, Nir Ben-Tal, Yana Bromberg, Tatyana Goldberg, László Kaján, Seán I. O'Donoghue, Chris Sander, Andrea Schafferhans, Avner Schlessinger, Gerrit Vriend, Milot Mirdita, Piotr Gawron, Wei Gu, Yohan Jarosz, Christophe Trefois, Martin Steinegger, Reinhard Schneider, Burkhard Rost

Nucleic Acids Res., 2021

2018

A Critical Note on Symmetry Contact Artifacts and the Evaluation of the Quality of Homology Models.

Dipali Singh, Karen R. M. Berntsen, Coos Baakman, Gert Vriend, Tapobrata Lahiri

Symmetry, 2018

Bio-knowledge-based filters improve residue-residue contact prediction accuracy.

Pawel P. Wozniak, J. Pelc, M. Skrzypecki, Gert Vriend, Malgorzata Kotulska

Bioinform., 2018

2017

3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine.

Ross McGuire, Stefan Verhoeven, Márton Vass, Gerrit Vriend, Iwan J. P. de Esch, Scott J. Lusher, Rob Leurs, Lars Ridder, Albert J. Kooistra, Tina Ritschel, Chris de Graaf

J. Chem. Inf. Model., 2017

Molden 2.0: quantum chemistry meets proteins.

Gijs Schaftenaar, Elias Vlieg, Gert Vriend

J. Comput. Aided Mol. Des., 2017

Correlated mutations select misfolded from properly folded proteins.

Pawel P. Wozniak, Gert Vriend, Malgorzata Kotulska

Bioinform., 2017

Forecasting residue-residue contact prediction accuracy.

Pawel P. Wozniak, Bogumil Konopka, J. Xu, Gert Vriend, Malgorzata Kotulska

Bioinform., 2017

2016

iPPI-DB: an online database of modulators of protein-protein interactions.

Céline M. Labbé, Mélaine A. Kuenemann, Barbara Zarzycka, Gert Vriend, Gerry A. F. Nicolaes, David Lagorce, Maria A. Miteva, Bruno O. Villoutreix, Olivier Sperandio

Nucleic Acids Res., 2016

Tools and data services registry: a community effort to document bioinformatics resources.

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

Nucleic Acids Res., 2016

GPCRdb: an information system for G protein-coupled receptors.

Vignir Ísberg, Stefan Mordalski, Christian Munk, Krzysztof Rataj, Kasper Harpsøe, Alexander S. Hauser, Bas Vroling, Andrzej J. Bojarski, Gert Vriend, David E. Gloriam

Nucleic Acids Res., 2016

KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins.

Joanna Lange, Lucjan Stanislaw Wyrwicz, Gert Vriend

Bioinform., 2016

2015

A series of PDB-related databanks for everyday needs.

Wouter G. Touw, Coos Baakman, Jon Black, Tim A. H. te Beek, Elmar Krieger, Robbie P. Joosten, Gert Vriend

Nucleic Acids Res., 2015

Discovery of Small Molecule CD40-TRAF6 Inhibitors.

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

J. Chem. Inf. Model., 2015

New ways to boost molecular dynamics simulations.

Elmar Krieger, Gert Vriend

J. Comput. Chem., 2015

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

Patricia C. Babbitt, Pantelis G. Bagos, Amos Bairoch, Alex Bateman, Arnaud Chatonnet, Mark Jinan Chen, David J. Craik, Robert D. Finn, David E. Gloriam, Daniel H. Haft, Bernard Henrissat, Gemma L. Holliday, Vignir Ísberg, Quentin Kaas, David Landsman, Nicolas Lenfant, Gerard Manning, Nozomi Nagano, Narayanaswamy Srinivasan, Claire O'Donovan, Kim D. Pruitt, Ramanathan Sowdhamini, Neil D. Rawlings, Milton H. Saier Jr., Joanna L. Sharman, Michael Spedding, Konstantinos D. Tsirigos, Åke Västermark, Gerrit Vriend

Database J. Biol. Databases Curation, 2015

Blind and Visually Impaired Students Can Perform Computer-Aided Molecular Design with an Assistive Molecular Fabricator.

Valère Lounnas, Henry B. Wedler, Timothy Newman, Jon Black, Gert Vriend

Proceedings of the Bioinformatics and Biomedical Engineering, 2015

2014

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

Nucleic Acids Res., 2014

GPCRDB: an information system for G protein-coupled receptors.

Vignir Ísberg, Bas Vroling, Rob van der Kant, Kang Li, Gert Vriend, David E. Gloriam

Nucleic Acids Res., 2014

Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol.

Valère Lounnas, Henry B. Wedler, Timothy Newman, Gijs Schaftenaar, Jason G. Harrison, Gabriella Nepomuceno, Ryan Pemberton, Dean J. Tantillo, Gert Vriend

J. Comput. Aided Mol. Des., 2014

YASARA View - molecular graphics for all devices - from smartphones to workstations.

Elmar Krieger, Gert Vriend

Bioinform., 2014

The NewProt Self-Service Portal for Protein Engineering.

Andreas Schwarte, Hanka Venselaar, Peter Haase, Gert Vriend

Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2014

2013

Status quo of annotation of human disease variants.

Hanka Venselaar, Franscesca Camilli, Shima Gholizadeh, Marlou Snelleman, Han G. Brunner, Gert Vriend

BMC Bioinform., 2013

2012

NucleaRDB: information system for nuclear receptors.

Bas Vroling, David Thorne, Philip McDermott, Henk-Jan Joosten, Teresa K. Attwood, Steve Pettifer, Gert Vriend

Nucleic Acids Res., 2012

NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.

Jurgen F. Doreleijers, Wim F. Vranken, Christopher F. Schulte, John L. Markley, Eldon L. Ulrich, Gert Vriend, Geerten W. Vuister

Nucleic Acids Res., 2012

AsteriX: A Web Server To Automatically Extract Ligand Coordinates from Figures in PDF Articles.

Valère Lounnas, Gert Vriend

J. Chem. Inf. Model., 2012

Drug design for ever, from hype to hope.

G. Seddon, Valère Lounnas, Ross McGuire, T. van den Bergh, Robert P. Bywater, Laerte Oliveira, Gert Vriend

J. Comput. Aided Mol. Des., 2012

WeNMR: Structural Biology on the Grid.

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

J. Grid Comput., 2012

2011

GPCRDB: information system for G protein-coupled receptors.

Bas Vroling, Marijn P. A. Sanders, Coos Baakman, Annika Borrmann, Stefan Verhoeven, Jan P. G. Klomp, Laerte Oliveira, Jacob de Vlieg, Gert Vriend

Nucleic Acids Res., 2011

A series of PDB related databases for everyday needs.

Robbie P. Joosten, Tim A. H. te Beek, Elmar Krieger, Maarten L. Hekkelman, Rob W. W. Hooft, Reinhard Schneider, Chris Sander, Gert Vriend

Nucleic Acids Res., 2011

Integrating GPCR-specific information with full text articles.

Bas Vroling, David Thorne, Philip McDermott, Teresa K. Attwood, Gert Vriend, Steve Pettifer

BMC Bioinform., 2011

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank.

Robbie P. Joosten, Krista Joosten, Serge X. Cohen, Gert Vriend, Anastassis Perrakis

Bioinform., 2011

WeNMR: Structural Biology on the Grid.

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

Proceedings of the 3rd International Workshop on Science Gateways for Life Sciences, 2011

2010

The EMBRACE web service collection.

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

Nucleic Acids Res., 2010

WIWS: a protein structure bioinformatics Web service collection.

Maarten L. Hekkelman, Tim A. H. te Beek, Steve Pettifer, David Thorne, Terri K. Attwood, Gert Vriend

Nucleic Acids Res., 2010

Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces.

Hanka Venselaar, Tim A. H. te Beek, Remko K. P. Kuipers, Maarten L. Hekkelman, Gert Vriend

BMC Bioinform., 2010

GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base.

George Khelashvili, Kevin C. Dorff, Jufang Shan, Marta Camacho-Artacho, Lucy Skrabanek, Bas Vroling, Michel Bouvier, Lakshmi Devi, Susan R. George, Jonathan A. Javitch, Martin J. Lohse, Graeme Milligan, Richard R. Neubig, Krzysztof Palczewski, Marc Parmentier, Jean-Philippe Pin, Gerrit Vriend, Fabien Campagne, Marta Filizola

Bioinform., 2010

2009

An active registry for bioinformatics web services.

Steve Pettifer, David Thorne, Philip McDermott, Terri K. Attwood, J. Baran, Jan Christian Bryne, Taavi Hupponen, D. Mowbray, Gert Vriend

Bioinform., 2009

2008

3D-Fun: predicting enzyme function from structure.

Marcin von Grotthuss, Dariusz Plewczynski, Gert Vriend, Leszek Rychlewski

Nucleic Acids Res., 2008

Tracing evolutionary pressure.

Kai Ye, Gert Vriend, Adriaan P. IJzerman

Bioinform., 2008

2007

Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base.

Lucy Skrabanek, Marta Murcia, Michel Bouvier, Lakshmi Devi, Susan R. George, Martin J. Lohse, Graeme Milligan, Richard R. Neubig, Krzysztof Palczewski, Marc Parmentier, Jean-Philippe Pin, Gerrit Vriend, Jonathan A. Javitch, Fabien Campagne, Marta Filizola

BMC Bioinform., 2007

2006

Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors.

Sander B. Nabuurs, Chris A. E. M. Spronk, Geerten W. Vuister, Gert Vriend

PLoS Comput. Biol., 2006

Correcting ligands, metabolites, and pathways.

Martin A. Ott, Gert Vriend

BMC Bioinform., 2006

2005

MRS: a fast and compact retrieval system for biological data.

Maarten L. Hekkelman, Gert Vriend

Nucleic Acids Res., 2005

GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases.

Marc A. van Driel, K. Cuelenaere, P. P. C. W. Kemmeren, Jack A. M. Leunissen, Han G. Brunner, Gert Vriend

Nucleic Acids Res., 2005

2004

Invited Talk: Information Flux Through Proteins.

Gert Vriend

Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, 2004

2003

GPCRDB information system for G protein-coupled receptors.

Florence Horn, Emmanuel Bettler, Laerte Oliveira, Fabien Campagne, Fred E. Cohen, Gerrit Vriend

Nucleic Acids Res., 2003

NRMD: Nuclear Receptor Mutation Database.

Joost J. J. van Durme, Emmanuel Bettler, Simon Folkertsma, Florence Horn, Gert Vriend

Nucleic Acids Res., 2003

NRSAS: Nuclear Receptor Structure Analysis Servers.

Emmanuel Bettler, Roland Krause, Florence Horn, Gert Vriend

Nucleic Acids Res., 2003

Batch mode generation of residue-based diagrams of proteins.

Fabien Campagne, Emmanuel Bettler, Gert Vriend, Harel Weinstein

Bioinform., 2003

2002

Models@Home: distributed computing in bioinformatics using a screensaver based approach.

Elmar Krieger, Gert Vriend

Bioinform., 2002

2001

Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems.

Florence Horn, Gerrit Vriend, Fred E. Cohen

Nucleic Acids Res., 2001

A sequence and structural study of transmembrane helices.

Robert P. Bywater, David Thomas, Gert Vriend

J. Comput. Aided Mol. Des., 2001

1998

GPCRDB: an information system for G protein-coupled receptors.

Florence Horn, Jonathan Weare, Margot W. Beukers, S. Hörsch, Amos Bairoch, W. Chen, Øyvind Edvardsen, Fabien Campagne, Gert Vriend

Nucleic Acids Res., 1998

Homology modeling, model and software evaluation: three related resources.

Rolando Rodríguez, Glay Chinea, Nelia Lopez, Tirso Pons, Gert Vriend

Bioinform., 1998

Molecular modelling and macromolecular visualisation with WHAT IF.

Brigitte Altenberg, Gerrit Vriend

Proceedings of the German Conference on Bioinformatics, 1998

1997

Objectively judging the quality of a protein structure from a Ramachandran plot.

Rob W. W. Hooft, Chris Sander, Gert Vriend

Comput. Appl. Biosci., 1997

1996

PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules.

Daan M. F. van Aalten, Robert P. Bywater, John B. C. Findlay, Manfred Hendlich, Rob W. W. Hooft, Gert Vriend

J. Comput. Aided Mol. Des., 1996

The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value.

Rob W. W. Hooft, Chris Sander, Michael Scharf, Gert Vriend

Comput. Appl. Biosci., 1996

1993

Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases.

Gert Vriend, Vincent Eijsink

J. Comput. Aided Mol. Des., 1993

A common motif in G-protein-coupled seven transmembrane helix receptors.

Laerte Oliveira, A. C. M. Paiva, Gert Vriend

J. Comput. Aided Mol. Des., 1993