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ORCIDGert Vriend
Gerrit Vriend
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- affiliation: Radboud University, Nijmegen Center for Molecular Life Sciences
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Journal Articles
- 2021
[j55]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:
PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Res. 49(Webserver-Issue): 535-540 (2021)- 2018
- [j54]Pawel P. Wozniak, J. Pelc, M. Skrzypecki, Gert Vriend, Malgorzata Kotulska:
Bio-knowledge-based filters improve residue-residue contact prediction accuracy. Bioinform. 34(21): 3675-3683 (2018) - [j53]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): 25 (2018) - 2017
- [j52]Pawel P. Wozniak, Gert Vriend, Malgorzata Kotulska:
Correlated mutations select misfolded from properly folded proteins. Bioinform. 33(10): 1497-1504 (2017) - [j51]Pawel P. Wozniak, Bogumil Konopka, J. Xu, Gert Vriend, Malgorzata Kotulska:
Forecasting residue-residue contact prediction accuracy. Bioinform. 33(21): 3405-3414 (2017) - [j50]Gijs Schaftenaar, Elias Vlieg, Gert Vriend:
Molden 2.0: quantum chemistry meets proteins. J. Comput. Aided Mol. Des. 31(9): 789-800 (2017) - [j49]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:
3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine. J. Chem. Inf. Model. 57(2): 115-121 (2017) - 2016
- [j48]Joanna Lange, Lucjan Stanislaw Wyrwicz, Gert Vriend:
KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins. Bioinform. 32(6): 932-936 (2016) - [j47]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:
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44(Database-Issue): 38-47 (2016) - [j46]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): 356-364 (2016) - [j45]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): 542-547 (2016) - 2015
- [j44]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:
Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. Database J. Biol. Databases Curation 2015 (2015) - [j43]Elmar Krieger, Gert Vriend:
New ways to boost molecular dynamics simulations. J. Comput. Chem. 36(13): 996-1007 (2015) - [j42]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): 294-307 (2015) - [j41]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): 364-368 (2015) - 2014
- [j40]Elmar Krieger, Gert Vriend:
YASARA View - molecular graphics for all devices - from smartphones to workstations. Bioinform. 30(20): 2981-2982 (2014) - [j39]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): 1057-1067 (2014) - [j38]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): 422-425 (2014) - [j37]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:
PredictProtein - an open resource for online prediction of protein structural and functional features. Nucleic Acids Res. 42(Webserver-Issue): 337-343 (2014) - 2013
- [j36]Hanka Venselaar, Franscesca Camilli, Shima Gholizadeh, Marlou Snelleman, Han G. Brunner, Gert Vriend:
Status quo of annotation of human disease variants. BMC Bioinform. 14: 352 (2013) - 2012
- [j35]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:
WeNMR: Structural Biology on the Grid. J. Grid Comput. 10(4): 743-767 (2012) - [j34]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): 137-150 (2012) - [j33]Valère Lounnas, Gert Vriend:
AsteriX: A Web Server To Automatically Extract Ligand Coordinates from Figures in PDF Articles. J. Chem. Inf. Model. 52(2): 568-576 (2012) - [j32]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): 377-380 (2012) - [j31]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): 519-524 (2012) - 2011
- [j30]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): 3392-3398 (2011) - [j29]Bas Vroling, David Thorne, Philip McDermott, Teresa K. Attwood, Gert Vriend, Steve Pettifer:
Integrating GPCR-specific information with full text articles. BMC Bioinform. 12: 362 (2011) - [j28]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): 309-319 (2011) - [j27]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): 411-419 (2011) - 2010
- [j26]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:
GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base. Bioinform. 26(14): 1804-1805 (2010) - [j25]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: 548 (2010) - [j24]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): 683-688 (2010) - [j23]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): 719-723 (2010) - 2009
- [j22]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): 2090-2091 (2009) - 2008
- [j21]Kai Ye, Gert Vriend, Adriaan P. IJzerman:
Tracing evolutionary pressure. Bioinform. 24(7): 908-915 (2008) - [j20]Marcin von Grotthuss, Dariusz Plewczynski, Gert Vriend, Leszek Rychlewski:
3D-Fun: predicting enzyme function from structure. Nucleic Acids Res. 36(Web-Server-Issue): 303-307 (2008) - 2007
- [j19]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:
Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base. BMC Bioinform. 8 (2007) - 2006
- [j18]Martin A. Ott, Gert Vriend:
Correcting ligands, metabolites, and pathways. BMC Bioinform. 7: 517 (2006) - [j17]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) - 2005
- [j16]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): 758-761 (2005) - [j15]Maarten L. Hekkelman, Gert Vriend:
MRS: a fast and compact retrieval system for biological data. Nucleic Acids Res. 33(Web-Server-Issue): 766-769 (2005) - 2003
- [j14]Fabien Campagne, Emmanuel Bettler, Gert Vriend, Harel Weinstein:
Batch mode generation of residue-based diagrams of proteins. Bioinform. 19(14): 1854-1855 (2003) - [j13]Florence Horn, Emmanuel Bettler, Laerte Oliveira, Fabien Campagne, Fred E. Cohen, Gerrit Vriend:
GPCRDB information system for G protein-coupled receptors. Nucleic Acids Res. 31(1): 294-297 (2003) - [j12]Joost J. J. van Durme, Emmanuel Bettler, Simon Folkertsma, Florence Horn, Gert Vriend:
NRMD: Nuclear Receptor Mutation Database. Nucleic Acids Res. 31(1): 331-333 (2003) - [j11]Emmanuel Bettler, Roland Krause, Florence Horn, Gert Vriend:
NRSAS: Nuclear Receptor Structure Analysis Servers. Nucleic Acids Res. 31(13): 3400-3403 (2003) - 2002
- [j10]Elmar Krieger, Gert Vriend:
Models@Home: distributed computing in bioinformatics using a screensaver based approach. Bioinform. 18(2): 315-318 (2002) - 2001
- [j9]Robert P. Bywater, David Thomas, Gert Vriend:
A sequence and structural study of transmembrane helices. J. Comput. Aided Mol. Des. 15(6): 533-552 (2001) - [j8]Florence Horn, Gerrit Vriend, Fred E. Cohen:
Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems. Nucleic Acids Res. 29(1): 346-349 (2001) - 1998
- [j7]Rolando Rodríguez, Glay Chinea, Nelia Lopez, Tirso Pons, Gert Vriend:
Homology modeling, model and software evaluation: three related resources. Bioinform. 14(6): 523-528 (1998) - [j6]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): 275-279 (1998) - 1997
- [j5]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): 425-430 (1997) - 1996
- [j4]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): 525-529 (1996) - [j3]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): 255-262 (1996) - 1993
- [j2]Gert Vriend, Vincent Eijsink:
Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases. J. Comput. Aided Mol. Des. 7(4): 367-396 (1993) - [j1]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): 649-658 (1993)
Conference and Workshop Papers
- 2015
- [c5]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: 18-29 - 2014
- [c4]Andreas Schwarte, Hanka Venselaar, Peter Haase, Gert Vriend:
The NewProt Self-Service Portal for Protein Engineering. SWAT4LS 2014 - 2011
- [c3]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:
WeNMR: Structural Biology on the Grid. IWSG-Life 2011 - 2004
- [c2]Gert Vriend:
Invited Talk: Information Flux Through Proteins. German Conference on Bioinformatics 2004: 121-122 - 1998
- [c1]Brigitte Altenberg, Gerrit Vriend:
Molecular modelling and macromolecular visualisation with WHAT IF. German Conference on Bioinformatics 1998
Coauthor Index
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