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)

Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases. - Gert Vriend; Vincent Eijsink (J. Comput. Aided Mol. Des., 1993)

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)

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)

Objectively judging the quality of a protein structure from a Ramachandran plot. - Rob W. W. Hooft; Chris Sander; Gert Vriend (Comput. Appl. Biosci., 1997)

Molecular modelling and macromolecular visualisation with WHAT IF. - Brigitte Altenberg; Gerrit Vriend (German Conference on Bioinformatics, 1998)

Homology modeling, model and software evaluation: three related resources. - Rolando Rodríguez; Glay Chinea; Nelia Lopez; Tirso Pons; Gert Vriend (Bioinform., 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)

A sequence and structural study of transmembrane helices. - Robert P. Bywater; David Thomas; Gert Vriend (J. Comput. Aided Mol. Des., 2001)

Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems. - Florence Horn; Gerrit Vriend; Fred E. Cohen (Nucleic Acids Res., 2001)

Models@Home: distributed computing in bioinformatics using a screensaver based approach. - Elmar Krieger; Gert Vriend (Bioinform., 2002)

Batch mode generation of residue-based diagrams of proteins. - Fabien Campagne; Emmanuel Bettler; Gert Vriend; Harel Weinstein (Bioinform., 2003)

NRSAS: Nuclear Receptor Structure Analysis Servers. - Emmanuel Bettler; Roland Krause; Florence Horn; Gert 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)

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)

Invited Talk: Information Flux Through Proteins. - Gert Vriend (German Conference on Bioinformatics, 2004)

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)

MRS: a fast and compact retrieval system for biological data. - Maarten L. Hekkelman; Gert Vriend (Nucleic Acids Res., 2005)

Correcting ligands, metabolites, and pathways. - Martin A. Ott; Gert Vriend (BMC Bioinform., 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)

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; et al. (BMC Bioinform., 2007)

Tracing evolutionary pressure. - Kai Ye 001; Gert Vriend; Adriaan P. IJzerman (Bioinform., 2008)

3D-Fun: predicting enzyme function from structure. - Marcin von Grotthuss; Dariusz Plewczynski; Gert Vriend; Leszek Rychlewski (Nucleic Acids Res., 2008)

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)

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; et al. (Bioinform., 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)

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)

The EMBRACE web service collection. - Steve Pettifer; Jon C. Ison; Matús Kalas; Dave Thorne; Philip McDermott; Inge Jonassen; Ali Liaquat; José María Fernández 001; José Manuel Rodriguez; David G. Pisano; Christophe Blanchet; Mahmut Uludag; et al. (Nucleic Acids Res., 2010)

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 002; Lucio Ferella; Antonio Rosato; Ivano Bertini; et al. (IWSG-Life, 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)

Integrating GPCR-specific information with full text articles. - Bas Vroling; David Thorne; Philip McDermott; Teresa K. Attwood; Gert Vriend; Steve Pettifer (BMC Bioinform., 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 002; Chris Sander; Gert Vriend (Nucleic Acids Res., 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)

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 002; Lucio Ferella; Antonio Rosato; Ivano Bertini; et al. (J. Grid Comput., 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)

AsteriX: A Web Server To Automatically Extract Ligand Coordinates from Figures in PDF Articles. - Valère Lounnas; Gert Vriend (J. Chem. Inf. Model., 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)

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)

Status quo of annotation of human disease variants. - Hanka Venselaar; Franscesca Camilli; Shima Gholizadeh; Marlou Snelleman; Han G. Brunner; Gert Vriend (BMC Bioinform., 2013)

The NewProt Self-Service Portal for Protein Engineering. - Andreas Schwarte; Hanka Venselaar; Peter Haase 001; Gert Vriend (SWAT4LS, 2014)

YASARA View - molecular graphics for all devices - from smartphones to workstations. - Elmar Krieger; Gert Vriend (Bioinform., 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)

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)

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; et al. (Nucleic Acids Res., 2014)

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 (IWBBIO (1), 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; et al. (Database J. Biol. Databases Curation, 2015)

New ways to boost molecular dynamics simulations. - Elmar Krieger; Gert Vriend (J. Comput. Chem., 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 004; Fabian Giehler; Arnd Kieser; et al. (J. Chem. Inf. Model., 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)

KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins. - Joanna Lange; Lucjan Stanislaw Wyrwicz; Gert Vriend (Bioinform., 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)

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; et al. (Nucleic Acids Res., 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)

Forecasting residue-residue contact prediction accuracy. - Pawel P. Wozniak; Bogumil Konopka; J. Xu; Gert Vriend; Malgorzata Kotulska (Bioinform., 2017)

Correlated mutations select misfolded from properly folded proteins. - Pawel P. Wozniak; Gert Vriend; Malgorzata Kotulska (Bioinform., 2017)

Molden 2.0: quantum chemistry meets proteins. - Gijs Schaftenaar; Elias Vlieg; Gert Vriend (J. Comput. Aided Mol. Des., 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)

Bio-knowledge-based filters improve residue-residue contact prediction accuracy. - Pawel P. Wozniak; J. Pelc; M. Skrzypecki; Gert Vriend; Malgorzata Kotulska (Bioinform., 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)

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; et al. (Nucleic Acids Res., 2021)