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Viewing Publication 1 - 49 from 49

2018

A Critical Note on Symmetry Contact Artifacts and the Evaluation of the Quality of Homology ModelsDipali Singh, Karen R. M. Berntsen, Coos Baakman, Gert Vriend, Tapobrata Lahiri. symmetry, 10(1):25, 2018. [doi]

Bio-knowledge-based filters improve residue-residue contact prediction accuracyPawel P. Wozniak, J. Pelc, M. Skrzypecki, Gert Vriend, Malgorzata Kotulska. bioinformatics, 34(21):3675-3683, 2018. [doi]

2017

Molden 2.0: quantum chemistry meets proteinsGijs Schaftenaar, Elias Vlieg, Gert Vriend. jcamd, 31(9):789-800, 2017. [doi]

Forecasting residue-residue contact prediction accuracyPawel P. Wozniak, Bogumil Konopka, J. Xu, Gert Vriend, Malgorzata Kotulska. bioinformatics, 33(21):3405-3414, 2017. [doi]

Correlated mutations select misfolded from properly folded proteinsPawel P. Wozniak, Gert Vriend, Malgorzata Kotulska. bioinformatics, 33(10):1497-1504, 2017. [doi]

2016

Tools and data services registry: a community effort to document bioinformatics resourcesJon 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 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. nar, 44(Database-Issue):38-47, 2016. [doi]

iPPI-DB: an online database of modulators of protein-protein interactionsCéline M. Labbé, Mélaine A. Kuenemann, Barbara Zarzycka, Gert Vriend, Gerry A. F. Nicolaes, David Lagorce, Maria A. Miteva, Bruno O. Villoutreix, Olivier Sperandio. nar, 44(Database-Issue):542-547, 2016. [doi]

KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteinsJoanna Lange, Lucjan Stanislaw Wyrwicz, Gert Vriend. bioinformatics, 32(6):932-936, 2016. [doi]

GPCRdb: an information system for G protein-coupled receptorsVignir Ísberg, Stefan Mordalski, Christian Munk, Krzysztof Rataj, Kasper Harpsøe, Alexander S. Hauser, Bas Vroling, Andrzej J. Bojarski, Gert Vriend, David E. Gloriam. nar, 44(Database-Issue):356-364, 2016. [doi]

2015

New ways to boost molecular dynamics simulationsElmar Krieger, Gert Vriend. jcc, 36(13):996-1007, 2015. [doi]

Blind and Visually Impaired Students Can Perform Computer-Aided Molecular Design with an Assistive Molecular FabricatorValère Lounnas, Henry B. Wedler, Timothy Newman, Jon Black, Gert Vriend. iwbbio 2015: 18-29 [doi]

A series of PDB-related databanks for everyday needsWouter G. Touw, Coos Baakman, Jon Black, Tim A. H. te Beek, Elmar Krieger, Robbie P. Joosten, Gert Vriend. nar, 43(Database-Issue):364-368, 2015. [doi]

Discovery of Small Molecule CD40-TRAF6 InhibitorsBarbara 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. jcisd, 55(2):294-307, 2015. [doi]

2014

2013

Status quo of annotation of human disease variantsHanka Venselaar, Franscesca Camilli, Shima Gholizadeh, Marlou Snelleman, Han G. Brunner, Gert Vriend. bmcbi, 14:352, 2013. [doi]

2012

NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDBJurgen F. Doreleijers, Wim F. Vranken, Christopher F. Schulte, John L. Markley, Eldon L. Ulrich, Gert Vriend, Geerten W. Vuister. nar, 40(Database-Issue):519-524, 2012. [doi]

AsteriX: A Web Server To Automatically Extract Ligand Coordinates from Figures in PDF ArticlesValère Lounnas, Gert Vriend. jcisd, 52(2):568-576, 2012. [doi]

Drug design for ever, from hype to hopeG. Seddon, V. Lounnas, R. McGuire, T. van den Bergh, Robert P. Bywater, Laerte Oliveira, Gert Vriend. jcamd, 26(1):137-150, 2012. [doi]

NucleaRDB: information system for nuclear receptorsBas Vroling, David Thorne, Philip McDermott, Henk-Jan Joosten, Teresa K. Attwood, Steve Pettifer, Gert Vriend. nar, 40(Database-Issue):377-380, 2012. [doi]

2011

Automatic rebuilding and optimization of crystallographic structures in the Protein Data BankRobbie P. Joosten, Krista Joosten, Serge X. Cohen, Gert Vriend, Anastassis Perrakis. bioinformatics, 27(24):3392-3398, 2011. [doi]

A series of PDB related databases for everyday needsRobbie P. Joosten, Tim A. H. te Beek, Elmar Krieger, Maarten L. Hekkelman, Rob W. W. Hooft, Reinhard Schneider, Chris Sander, Gert Vriend. nar, 39(Database-Issue):411-419, 2011. [doi]

GPCRDB: information system for G protein-coupled receptorsBas Vroling, Marijn P. A. Sanders, Coos Baakman, Annika Borrmann, Stefan Verhoeven, Jan P. G. Klomp, Laerte Oliveira, Jacob de Vlieg, Gert Vriend. nar, 39(Database-Issue):309-319, 2011. [doi]

Integrating GPCR-specific information with full text articlesBas Vroling, David Thorne, Philip McDermott, Teresa K. Attwood, Gert Vriend, Steve Pettifer. bmcbi, 12:362, 2011. [doi]

2010

WIWS: a protein structure bioinformatics Web service collectionMaarten L. Hekkelman, Tim A. H. te Beek, Steve Pettifer, David Thorne, Terri K. Attwood, Gert Vriend. nar, 38(Web-Server-Issue):719-723, 2010. [doi]

Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfacesHanka Venselaar, Tim A. H. te Beek, Remko K. P. Kuipers, Maarten L. Hekkelman, Gert Vriend. bmcbi, 11:548, 2010. [doi]

2008

3D-Fun: predicting enzyme function from structureMarcin von Grotthuss, Dariusz Plewczynski, Gert Vriend, Leszek Rychlewski. nar, 36(Web-Server-Issue):303-307, 2008. [doi]

Tracing evolutionary pressureKai Ye, Gert Vriend, Adriaan P. IJzerman. bioinformatics, 24(7):908-915, 2008. [doi]

2006

Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major ErrorsSander B. Nabuurs, Chris A. E. M. Spronk, Geerten W. Vuister, Gert Vriend. ploscb, 2(2), 2006. [doi]

Correcting ligands, metabolites, and pathwaysMartin A. Ott, Gert Vriend. bmcbi, 7:517, 2006. [doi]

2005

GeneSeeker: extraction and integration of human disease-related information from web-based genetic databasesM. A. van Driel, K. Cuelenaere, P. P. C. W. Kemmeren, J. A. M. Leunissen, H. G. Brunner, Gert Vriend. nar, 33(Web-Server-Issue):758-761, 2005. [doi]

2004

Invited Talk: Information Flux Through ProteinsGert Vriend. gcb 2004: 121-122

2003

NRSAS: Nuclear Receptor Structure Analysis ServersEmmanuel Bettler, Roland Krause, Florence Horn, Gert Vriend. nar, 31(13):3400-3403, 2003.

Batch mode generation of residue-based diagrams of proteinsFabien Campagne, Emmanuel Bettler, Gert Vriend, Harel Weinstein. bioinformatics, 19(14):1854-1855, 2003.

NRMD: Nuclear Receptor Mutation DatabaseJoost J. J. van Durme, Emmanuel Bettler, Simon Folkertsma, Florence Horn, Gert Vriend. nar, 31(1):331-333, 2003.

2002

Models@Home: distributed computing in bioinformatics using a screensaver based approachElmar Krieger, Gert Vriend. bioinformatics, 18(2):315-318, 2002.

2001

A sequence and structural study of transmembrane helicesRobert P. Bywater, David Thomas, Gert Vriend. jcamd, 15(6):533-552, 2001. [doi]

1998

GPCRDB: an information system for G protein-coupled receptorsFlorence Horn, J. Weare, Margot W. Beukers, S. Hörsch, Amos Bairoch, W. Chen, Øyvind Edvardsen, Fabien Campagne, Gert Vriend. nar, 26(1):275-279, 1998.

Homology modeling, model and software evaluation: three related resourcesR. Rodriguez, G. Chinea, N. Lopez, T. Pons, Gert Vriend. bioinformatics, 14(6):523-528, 1998.

1997

Objectively judging the quality of a protein structure from a Ramachandran plotR. W. Hooft, Chris Sander, Gert Vriend. bioinformatics, 13(4):425-430, 1997.

1996

The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added valueR. W. Hooft, Chris Sander, Michael Scharf, Gert Vriend. bioinformatics, 12(6):525-529, 1996.

PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small moleculesDaan M. F. van Aalten, Robert P. Bywater, John B. C. Findlay, Manfred Hendlich, Rob W. W. Hooft, Gert Vriend. jcamd, 10(3):255-262, 1996.

1993

A common motif in G-protein-coupled seven transmembrane helix receptorsL. Oliveira, A. C. M. Paiva, Gert Vriend. jcamd, 7(6):649-658, 1993.

Prediction and analysis of structure, stability and unfolding of thermolysin-like proteasesGert Vriend, Vincent Eijsink. jcamd, 7(4):367-396, 1993.

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