Gert Vriend

Gert Vriend

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Gert Vriend

Publications by authors named "Gert Vriend"

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G protein-coupled receptors of class A harness the energy of membrane potential to increase their sensitivity and selectivity.

Biochim Biophys Acta Biomembr 2019 Dec 23;1861(12):183051. Epub 2019 Aug 23.

School of Physics, Osnabrueck University, 49069 Osnabrück, Germany; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia; School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia. Electronic address:

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http://dx.doi.org/10.1016/j.bbamem.2019.183051DOI Listing
December 2019

Loop modelling 1.0.

J Mol Graph Model 2018 09 7;84:64-68. Epub 2018 Jun 7.

Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-175, Tehran, Iran. Electronic address:

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http://dx.doi.org/10.1016/j.jmgm.2018.06.001DOI Listing
September 2018

3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery.

ChemMedChem 2018 03 14;13(6):614-626. Epub 2018 Feb 14.

Division of Medicinal Chemistry, Faculty of Science, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/cmdc.201700754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5900740PMC
March 2018

Aggregation of population-based genetic variation over protein domain homologues and its potential use in genetic diagnostics.

Hum Mutat 2017 11 31;38(11):1454-1463. Epub 2017 Aug 31.

Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, GA, 6525, The Netherlands.

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http://doi.wiley.com/10.1002/humu.23313
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http://dx.doi.org/10.1002/humu.23313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5656839PMC
November 2017

Molden 2.0: quantum chemistry meets proteins.

J Comput Aided Mol Des 2017 Sep 27;31(9):789-800. Epub 2017 Jul 27.

CMBI, Radboudumc, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1007/s10822-017-0042-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5633641PMC
September 2017

NewProt - a protein engineering portal.

Protein Eng Des Sel 2017 06;30(6):441-447

CMBI, Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/protein/gzx024DOI Listing
June 2017

Outer membrane phospholipase A's roles in acid adaptation.

Gut Pathog 2017 12;9:36. Epub 2017 Jun 12.

Norwegian Institute of Public Health, Box 4404, Nydalen, 0403 Oslo, Norway.

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http://dx.doi.org/10.1186/s13099-017-0184-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5469174PMC
June 2017

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

Nucleic Acids Res 2017 03;45(5):2936

Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1093/nar/gkw1218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389621PMC
March 2017

Validation and correction of Zn-CysHis complexes.

Acta Crystallogr D Struct Biol 2016 10 15;72(Pt 10):1110-1118. Epub 2016 Sep 15.

Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

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http://dx.doi.org/10.1107/S2059798316013036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5053137PMC
October 2016

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

Bioinformatics 2016 03 14;32(6):932-6. Epub 2015 Nov 14.

CMBI Radboudumc, 6525 GA, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btv663DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4803389PMC
March 2016

New Biological Insights from Better Structure Models.

J Mol Biol 2016 Mar 8;428(6):1375-1393. Epub 2016 Feb 8.

Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2016.02.002DOI Listing
March 2016

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

Nucleic Acids Res 2016 Jan 1;44(D1):D542-7. Epub 2015 Oct 1.

Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques, In Silico, INSERM UMR-S 973, Paris, France INSERM, U973, Paris, France

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http://dx.doi.org/10.1093/nar/gkv982DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702945PMC
January 2016

Stabilization of protein-protein interaction complexes through small molecules.

Drug Discov Today 2016 Jan 3;21(1):48-57. Epub 2015 Oct 3.

Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France; Faculté de Pharmacie, CDithem, 1 rue du Prof. Laguesse, 59000 Lille, France. Electronic address:

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http://dx.doi.org/10.1016/j.drudis.2015.09.011DOI Listing
January 2016

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

Nucleic Acids Res 2016 Jan 3;44(D1):D38-47. Epub 2015 Nov 3.

Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.

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http://dx.doi.org/10.1093/nar/gkv1116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702812PMC
January 2016

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

Nucleic Acids Res 2016 Jan 17;44(D1):D356-64. Epub 2015 Nov 17.

Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark

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http://dx.doi.org/10.1093/nar/gkv1178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702843PMC
January 2016

Detection of trans-cis flips and peptide-plane flips in protein structures.

Acta Crystallogr D Biol Crystallogr 2015 Aug 28;71(Pt 8):1604-14. Epub 2015 Jul 28.

Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1107/S1399004715008263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528797PMC
August 2015

New ways to boost molecular dynamics simulations.

J Comput Chem 2015 May 30;36(13):996-1007. Epub 2015 Mar 30.

Centre for Molecular and Biomolecular Informatics, Radboudumc, PO Box 9101, 6500 HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.1002/jcc.23899DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6680170PMC
May 2015

Quantum chemical study of the isomerization of 24-methylenecycloartanol, a potential marker of olive oil refining.

J Mol Model 2015 May 10;21(5):111. Epub 2015 Apr 10.

Department of Chemistry, University of California-Davis, Davis, CA, 95616, USA.

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http://dx.doi.org/10.1007/s00894-015-2652-yDOI Listing
May 2015

Discovery of small molecule CD40-TRAF6 inhibitors.

J Chem Inf Model 2015 Feb 27;55(2):294-307. Epub 2015 Jan 27.

Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University , 6200 MD Maastricht, The Netherlands.

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http://dx.doi.org/10.1021/ci500631eDOI Listing
February 2015

A series of PDB-related databanks for everyday needs.

Nucleic Acids Res 2015 Jan 28;43(Database issue):D364-8. Epub 2014 Oct 28.

Centre for Molecular and Biomolecular Informatics, CMBI, Radboud university medical center, Geert Grooteplein Zuid 26-28 6525 GA Nijmegen, The Netherlands

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http://swift.cmbi.ru.nl/gv/facilities/HTML/facilities.pdf
Web Search
http://nar.oxfordjournals.org/content/early/2014/10/28/nar.g
Web Search
http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gku1028
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http://dx.doi.org/10.1093/nar/gku1028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383885PMC
January 2015

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 2014 Nov 5;28(11):1057-67. Epub 2014 Aug 5.

CMBI Radboudumc, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands,

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http://dx.doi.org/10.1007/s10822-014-9782-7DOI Listing
November 2014

BDB: databank of PDB files with consistent B-factors.

Protein Eng Des Sel 2014 Nov;27(11):457-62

Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Center, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands

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http://dx.doi.org/10.1093/protein/gzu044DOI Listing
November 2014

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

Bioinformatics 2014 Oct 4;30(20):2981-2. Epub 2014 Jul 4.

Centre for Molecular and Biomolecular Informatics, NCMLS, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, the Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btu426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184264PMC
October 2014

Alpha-bulges in G protein-coupled receptors.

Int J Mol Sci 2014 May 6;15(5):7841-64. Epub 2014 May 6.

Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.3390/ijms15057841DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4057707PMC
May 2014

Anomalies in the refinement of isoleucine.

Acta Crystallogr D Biol Crystallogr 2014 Apr 19;70(Pt 4):1037-49. Epub 2014 Mar 19.

CMBI, Radboud University Medical Center, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1107/S139900471400087XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975889PMC
April 2014

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

Nucleic Acids Res 2014 Jan 3;42(Database issue):D422-5. Epub 2013 Dec 3.

Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark, Bio-Prodict B.V., Castellastraat 116, 6512 EZ, Nijmegen, The Netherlands and CMBI, NCMLS, Radboudumc Nijmegen Medical Centre, Geert Grooteplein Zuid 26-28, 6525 GA, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkt1255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965068PMC
January 2014

Status quo of annotation of human disease variants.

BMC Bioinformatics 2013 Dec 4;14:352. Epub 2013 Dec 4.

CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Nijmegen, PO Box 9101, Nijmegen, HB 6500, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-14-352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234487PMC
December 2013

Consensus engineering of sucrose phosphorylase: the outcome reflects the sequence input.

Biotechnol Bioeng 2013 Oct 7;110(10):2563-72. Epub 2013 May 7.

Department of Biochemical and Microbial Technology, Centre for Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.

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http://dx.doi.org/10.1002/bit.24940DOI Listing
October 2013

A molecular switch driving inactivation in the cardiac K+ channel HERG.

PLoS One 2012 24;7(7):e41023. Epub 2012 Jul 24.

Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0041023PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3404103PMC
April 2013

CING: an integrated residue-based structure validation program suite.

J Biomol NMR 2012 Nov 18;54(3):267-83. Epub 2012 Sep 18.

CMBI, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1007/s10858-012-9669-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483101PMC
November 2012

Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.

PLoS One 2012 11;7(5):e33931. Epub 2012 May 11.

Theoretische und computergestützte Biophysik, Max-Planck-Institut für biophysikalische Chemie, Göttingen, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0033931PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3350514PMC
October 2012

NucleaRDB: information system for nuclear receptors.

Nucleic Acids Res 2012 Jan 7;40(Database issue):D377-80. Epub 2011 Nov 7.

CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Nijmegen, Bio-Prodict, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkr960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245090PMC
January 2012

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

Nucleic Acids Res 2012 Jan 1;40(Database issue):D519-24. Epub 2011 Dec 1.

IMM, Radboud University Nijmegen, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkr1134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245154PMC
January 2012

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

Bioinformatics 2011 Dec 27;27(24):3392-8. Epub 2011 Oct 27.

Department of Biochemistry, NKI, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btr590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232375PMC
December 2011

Integrating GPCR-specific information with full text articles.

BMC Bioinformatics 2011 Sep 12;12:362. Epub 2011 Sep 12.

CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, Nijmegen, 6525 GA, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-12-362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179973PMC
September 2011

GPCRDB: information system for G protein-coupled receptors.

Nucleic Acids Res 2011 Jan 2;39(Database issue):D309-19. Epub 2010 Nov 2.

CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkq1009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013641PMC
January 2011

A series of PDB related databases for everyday needs.

Nucleic Acids Res 2011 Jan 11;39(Database issue):D411-9. Epub 2010 Nov 11.

Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkq1105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013697PMC
January 2011

On the complexity of Engh and Huber refinement restraints: the angle τ as example.

Acta Crystallogr D Biol Crystallogr 2010 Dec 16;66(Pt 12):1341-50. Epub 2010 Nov 16.

Centre for Molecular and Biomolecular Informatics (CMBI), Nijmegen Centre for Molecular Life Sciences (NCMLS), Radboud University Nijmegen Medical Centre, 6525GA 26 Nijmegen, The Netherlands.

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http://dx.doi.org/10.1107/S0907444910040928DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995724PMC
December 2010

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

BMC Bioinformatics 2010 Nov 8;11:548. Epub 2010 Nov 8.

CMBI, NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, Netherlands.

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http://dx.doi.org/10.1186/1471-2105-11-548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2992548PMC
November 2010

The moonlighting function of pyruvate carboxylase resides in the non-catalytic end of the TIM barrel.

Biochim Biophys Acta 2010 Sep 30;1803(9):1038-42. Epub 2010 Mar 30.

Department of Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), Kluyver Centre for Genomics of Industrial Fermentation, University of Groningen, NL-9750 AA Haren, The Netherlands.

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http://dx.doi.org/10.1016/j.bbamcr.2010.03.018DOI Listing
September 2010

3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities.

Proteins 2010 Jul;78(9):2101-13

Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1002/prot.22725DOI Listing
July 2010

Homology modelling and spectroscopy, a never-ending love story.

Eur Biophys J 2010 Mar 29;39(4):551-63. Epub 2009 Aug 29.

Centre for Molecular and Biomolecular Informatics, CMBI, NCMLS 260, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.1007/s00249-009-0531-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841279PMC
March 2010

Toward a consensus model of the HERG potassium channel.

ChemMedChem 2010 Mar;5(3):455-67

Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

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http://dx.doi.org/10.1002/cmdc.200900461DOI Listing
March 2010

The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries.

J Biomol NMR 2009 Dec 7;45(4):389-96. Epub 2009 Oct 7.

Radboud University Medical Centre Nijmegen, Geert Grooteplein 26-28, HB, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1007/s10858-009-9378-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777234PMC
December 2009

Correlated mutation analyses on super-family alignments reveal functionally important residues.

Proteins 2009 Aug;76(3):608-16

Centre of Molecular and Biomolecular Informatics, Radboud University, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1002/prot.22374DOI Listing
August 2009

Re-refinement from deposited X-ray data can deliver improved models for most PDB entries.

Acta Crystallogr D Biol Crystallogr 2009 Feb 20;65(Pt 2):176-85. Epub 2009 Jan 20.

CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1107/S0907444908037591DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631631PMC
February 2009

3D-Fun: predicting enzyme function from structure.

Nucleic Acids Res 2008 Jul 30;36(Web Server issue):W303-7. Epub 2008 May 30.

CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkn308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447717PMC
July 2008

The molecular mechanism of toxin-induced conformational changes in a potassium channel: relation to C-type inactivation.

Structure 2008 May;16(5):747-54

Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

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http://dx.doi.org/10.1016/j.str.2008.01.018DOI Listing
May 2008

Tracing evolutionary pressure.

Bioinformatics 2008 Apr 26;24(7):908-15. Epub 2008 Feb 26.

Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btn057DOI Listing
April 2008

PDB improvement starts with data deposition.

Science 2007 Jul;317(5835):195-6

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http://dx.doi.org/10.1126/science.317.5835.195DOI Listing
July 2007

Stabilization of peptide fibrils by hydrophobic interaction.

Langmuir 2007 Feb;23(4):2058-63

Organic Chemistry, Institute for Molecules and Materials and Center for Molecular and Biomolecular Informatics, NCMLS, Radboud University Nijmegen, Toernooiveld 1- Huygens Building 03.016, 6525 ED Nijmegen, The Netherlands.

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http://dx.doi.org/10.1021/la0625345DOI Listing
February 2007

Fast empirical pKa prediction by Ewald summation.

J Mol Graph Model 2006 Dec 27;25(4):481-6. Epub 2006 Apr 27.

Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen, Toernooiveld 1, 6525ED Nijmegen, The Netherlands.

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http://linkinghub.elsevier.com/retrieve/pii/S109332630600047
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http://dx.doi.org/10.1016/j.jmgm.2006.02.009DOI Listing
December 2006

Negative constraints underlie the ErbB specificity of epidermal growth factor-like ligands.

J Biol Chem 2006 Dec 10;281(52):40033-40. Epub 2006 Oct 10.

Department of Cell Biology and Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen, Faculty of Science, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands.

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http://dx.doi.org/10.1074/jbc.M603168200DOI Listing
December 2006

Costs and benefits of processivity in enzymatic degradation of recalcitrant polysaccharides.

Proc Natl Acad Sci U S A 2006 Nov 20;103(48):18089-94. Epub 2006 Nov 20.

Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432 As, Norway.

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http://dx.doi.org/10.1073/pnas.0608909103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1838711PMC
November 2006

Correcting ligands, metabolites, and pathways.

BMC Bioinformatics 2006 Nov 28;7:517. Epub 2006 Nov 28.

Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
Publisher Site
http://dx.doi.org/10.1186/1471-2105-7-517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1686944PMC
November 2006

GRIS: glycoprotein-hormone receptor information system.

Mol Endocrinol 2006 Sep 16;20(9):2247-55. Epub 2006 Mar 16.

Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Campus Erasme, Route de Lennik 808, B-1070 Brussels, Belgium.

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http://dx.doi.org/10.1210/me.2006-0020DOI Listing
September 2006

A text-mining analysis of the human phenome.

Eur J Hum Genet 2006 May;14(5):535-42

Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen, Toernooiveld 1, 6525ED Nijmegen, the Netherlands.

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May 2006

Integrins of Anopheles gambiae and a putative role of a new beta integrin, BINT2, in phagocytosis of E. coli.

Insect Biochem Mol Biol 2006 Apr 19;36(4):282-90. Epub 2006 Jan 19.

European Molecular Biology Laboratory, 1 Meyerhofstrasse, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.ibmb.2006.01.004DOI Listing
April 2006

Traditional biomolecular structure determination by NMR spectroscopy allows for major errors.

PLoS Comput Biol 2006 Feb 3;2(2):e9. Epub 2006 Feb 3.

Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University, Nijmegen, Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.0020009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1359070PMC
February 2006

Definition of a new information-based per-residue quality parameter.

J Biomol NMR 2005 Oct;33(2):123-34

Center for Molecular and Biomolecular Informatics, NCMLS, Radboud University Nijmegen, Toernooiveld 1, 6525, ED, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1007/s10858-005-2826-5DOI Listing
October 2005

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

Nucleic Acids Res 2005 Jul;33(Web Server issue):W758-61

Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen, PO Box 9010, 6500GL Nijmegen, The Netherlands.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gki435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160196PMC
July 2005

Induced refolding of a temperature denatured llama heavy-chain antibody fragment by its antigen.

Proteins 2005 May;59(3):555-64

Department of Molecular and Cellular Biology, University of Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1002/prot.20378DOI Listing
May 2005

Isolation of llama antibody fragments for prevention of dandruff by phage display in shampoo.

Appl Environ Microbiol 2005 Jan;71(1):442-50

Department of Molecular and Cellular Biology, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.

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http://dx.doi.org/10.1128/AEM.71.1.442-450.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC544197PMC
January 2005

Making optimal use of empirical energy functions: force-field parameterization in crystal space.

Proteins 2004 Dec;57(4):678-83

Center for Molecular and Biomolecular Informatics, University of Nijmegen, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1002/prot.20251DOI Listing
December 2004

Protein design: quo vadis?

Authors:
Gert Vriend

Science 2004 Nov;306(5699):1135

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November 2004

Rational engineering of enzyme stability.

J Biotechnol 2004 Sep;113(1-3):105-20

Department of Chemistry, Biotechnology and Food Science, Agricultural University of Norway, PO Box 5040, N-1432 As.

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http://dx.doi.org/10.1016/j.jbiotec.2004.03.026DOI Listing
September 2004

Molecular determinants of the interaction of Mad with the PAH2 domain of mSin3.

J Biol Chem 2004 Jun 26;279(24):25823-9. Epub 2004 Mar 26.

Department of Molecular Biology, Centre for Molecular and Biomolecular Informatics, University of Nijmegen, 6500 HB Nijmegen, The Netherlands.

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June 2004

DRESS: a database of REfined solution NMR structures.

Proteins 2004 May;55(3):483-6

Center for Molecular and Biomolecular Informatics, University of Nijmegen, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1002/prot.20118DOI Listing
May 2004

Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase.

Eur J Biochem 2004 Jan;271(2):253-62

Department of Chemistry and Biotechnology, Agricultural University of Norway, As, Norway.

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http://dx.doi.org/10.1046/j.1432-1033.2003.03923.xDOI Listing
January 2004

Stabilization of a chitinase from Serratia marcescens by Gly-->Ala and Xxx-->Pro mutations.

Protein Eng 2003 Nov;16(11):841-6

Department of Chemistry and Biotechnology, Agricultural University of Norway, PO Box 5040, 1432 As, Norway.

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http://dx.doi.org/10.1093/protein/gzg105DOI Listing
November 2003

Quantitative evaluation of experimental NMR restraints.

J Am Chem Soc 2003 Oct;125(39):12026-34

Center for Molecular and Biomolecular Informatics, University of Nijmegen, The Netherlands.

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http://dx.doi.org/10.1021/ja035440fDOI Listing
October 2003

Batch mode generation of residue-based diagrams of proteins.

Bioinformatics 2003 Sep;19(14):1854-5

Institute for Computational Biomedicine and Department of Physiology and Biophysics, Mount Sinai School of Medicine, Box 1218, New York, NY 10029, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg236DOI Listing
September 2003

NRSAS: Nuclear Receptor Structure Analysis Servers.

Nucleic Acids Res 2003 Jul;31(13):3400-3

CMBI KUN, PO Box 9010, 6500 GL Nijmegen, The Netherlands.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168912PMC
http://dx.doi.org/10.1093/nar/gkg505DOI Listing
July 2003

Homology modeling.

Methods Biochem Anal 2003 ;44:509-23

Center for Molecular and Biomolecular Informatics, University of Nijmegen, Nijmegen, The Netherlands.

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April 2003

The precision of NMR structure ensembles revisited.

J Biomol NMR 2003 Mar;25(3):225-34

Centre for Molecular and Biomolecular Informatics, University of Nijmegen, The Netherlands.

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http://dx.doi.org/10.1023/a:1022819716110DOI Listing
March 2003

NRMD: Nuclear Receptor Mutation Database.

Nucleic Acids Res 2003 Jan;31(1):331-3

CMBI, University of Nijmegen, Nijmegen, The Netherlands.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165569PMC
http://dx.doi.org/10.1093/nar/gkg122DOI Listing
January 2003

Prediction of protein residue contacts with a PDB-derived likelihood matrix.

Protein Eng 2002 Sep;15(9):721-5

Section of Neurobiology, Yale University School of Medicine, New Haven, CT, USA.

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http://dx.doi.org/10.1093/protein/15.9.721DOI Listing
September 2002

The effects of modifying the surface charge on the catalytic activity of a thermolysin-like protease.

J Biol Chem 2002 May 21;277(18):15432-8. Epub 2002 Feb 21.

Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.

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May 2002

Increasing the precision of comparative models with YASARA NOVA--a self-parameterizing force field.

Proteins 2002 May;47(3):393-402

Center for Molecular and Biomolecular Informatics, Nijmegen, The Netherlands.

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May 2002