Josep Lluis Gelpí

Josep Lluis Gelpí

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Josep Lluis Gelpí

Josep Lluis Gelpí

Publications by authors named "Josep Lluis Gelpí"

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39Publications

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Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning.

Nucleic Acids Res 2019 10;47(18):9511-9523

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain.

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http://dx.doi.org/10.1093/nar/gkz759DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6765203PMC
October 2019

How B-DNA Dynamics Decipher Sequence-Selective Protein Recognition.

J Mol Biol 2019 09 17;431(19):3845-3859. Epub 2019 Jul 17.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain; Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.07.021DOI Listing
September 2019

Genetic variation at the glycosaminoglycan metabolism pathway contributes to the risk of psoriatic arthritis but not psoriasis.

Ann Rheum Dis 2019 03 14;78(3). Epub 2018 Dec 14.

Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain

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http://dx.doi.org/10.1136/annrheumdis-2018-214158DOI Listing
March 2019

Metadata to Describe Genomic Information.

Stud Health Technol Inform 2018 ;247:621-625

Barcelona Supercomputing Center (BSC).

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June 2018

The Multiple Roles of Waters in Protein Solvation.

J Phys Chem B 2017 04 20;121(15):3636-3643. Epub 2017 Jan 20.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12, Barcelona, 08028, Spain.

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http://dx.doi.org/10.1021/acs.jpcb.6b09676DOI Listing
April 2017

Structural and energetic study of cation-π-cation interactions in proteins.

Phys Chem Chem Phys 2017 Apr;19(15):9849-9861

Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica and Institut de Biomedicina (IBUB), Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.

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http://dx.doi.org/10.1039/c6cp08448fDOI Listing
April 2017

Long-timescale dynamics of the Drew-Dickerson dodecamer.

Nucleic Acids Res 2016 05 15;44(9):4052-66. Epub 2016 Apr 15.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain

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http://dx.doi.org/10.1093/nar/gkw264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4872116PMC
May 2016

PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.

J Chem Theory Comput 2015 Dec 20;11(12):5929-38. Epub 2015 Nov 20.

Institute for Research in Biomedicine (IRB Barcelona) , Baldiri i Reixac 10, Barcelona 08028, Spain.

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http://dx.doi.org/10.1021/acs.jctc.5b00660DOI Listing
December 2015

Inntags: small self-structured epitopes for innocuous protein tagging.

Nat Methods 2015 Oct 31;12(10):955-8. Epub 2015 Aug 31.

Molecular Biology Institute of Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.

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http://dx.doi.org/10.1038/nmeth.3556DOI Listing
October 2015

Effects of cadmium and mercury on the upper part of skeletal muscle glycolysis in mice.

PLoS One 2014 28;9(1):e80018. Epub 2014 Jan 28.

Department of Biochemistry and Molecular Biology and IBUB, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain ; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080018PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3904826PMC
December 2014

Exploring early stages of the chemical unfolding of proteins at the proteome scale.

PLoS Comput Biol 2013 12;9(12):e1003393. Epub 2013 Dec 12.

Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain ; Joint Research Program in Computational Biology, Institute for Research in Biomedicine and Barcelona Supercomputing Center, Barcelona, Spain ; Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain.

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http://dx.doi.org/10.1371/journal.pcbi.1003393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861036PMC
August 2014

NAFlex: a web server for the study of nucleic acid flexibility.

Nucleic Acids Res 2013 Jul 17;41(Web Server issue):W47-55. Epub 2013 May 17.

Institute for Research in Biomedicine, Molecular Modelling and Bioinformatics Department, 08028, Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkt378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3692121PMC
July 2013

Efficient Relaxation of Protein-Protein Interfaces by Discrete Molecular Dynamics Simulations.

J Chem Theory Comput 2013 Feb 28;9(2):1222-9. Epub 2012 Dec 28.

Institute for Research in Biomedicine (IRB Barcelona), Baldiri i Reixac 10, Barcelona 08028, Spain.

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http://dx.doi.org/10.1021/ct301039eDOI Listing
February 2013

Unveiling case-control relationships in designing a simple and powerful method for detecting gene-gene interactions.

Genet Epidemiol 2012 Nov 7;36(7):710-6. Epub 2012 Aug 7.

Rheumatology Research Group, Vall d'Hebron Research Insitute, Barcelona, Spain.

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http://dx.doi.org/10.1002/gepi.21665DOI Listing
November 2012

Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations.

J Chem Theory Comput 2012 Nov 6;8(11):4707-18. Epub 2012 Sep 6.

Joint IRB-BSC Program in Computational Biology, Institute of Research in Biomedicine, Josep Samitier 1-5, Barcelona, 08028, Spain.

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http://dx.doi.org/10.1021/ct300494qDOI Listing
November 2012

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.

Bioinformatics 2012 May 21;28(9):1278-9. Epub 2012 Mar 21.

Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/bts139DOI Listing
May 2012

MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.

Structure 2010 Nov;18(11):1399-409

Joint IRB-BSC Computational Biology Programme, Institute of Research in Biomedicine, Parc Científic de Barcelona, Baldiri Reixac 10, Barcelona 08028, Spain.

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http://dx.doi.org/10.1016/j.str.2010.07.013DOI Listing
November 2010

FlexServ: an integrated tool for the analysis of protein flexibility.

Bioinformatics 2009 Jul 7;25(13):1709-10. Epub 2009 May 7.

Joint IRB-BSC Program on Computational Biology, Institute of Research in Biomedicine, Barcelona Science Park, Josep Samitier 1-5, Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btp304DOI Listing
July 2009

Functional and structural characterization of the first prokaryotic member of the L-amino acid transporter (LAT) family: a model for APC transporters.

J Biol Chem 2007 May 6;282(18):13270-81. Epub 2007 Mar 6.

Institute for Research in Biomedicine, Barcelona Science Park and Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, E-08028 Barcelona, Spain.

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http://dx.doi.org/10.1074/jbc.M610695200DOI Listing
May 2007

A consensus view of protein dynamics.

Proc Natl Acad Sci U S A 2007 Jan 10;104(3):796-801. Epub 2007 Jan 10.

Molecular Modelling and Bioinformatics Unit, and Structural Biology Node, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1073/pnas.0605534104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1783393PMC
January 2007

Dissection of the recognition properties of p38 MAP kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor family.

J Med Chem 2007 Jan;50(2):283-93

Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain.

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http://dx.doi.org/10.1021/jm061073hDOI Listing
January 2007

A fast method for the determination of fractional contributions to solvation in proteins.

Protein Sci 2006 Nov 25;15(11):2525-33. Epub 2006 Sep 25.

Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica, Barcelona 08028, Spain.

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http://dx.doi.org/10.1110/ps.062406706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2242413PMC
November 2006

PMUT: a web-based tool for the annotation of pathological mutations on proteins.

Bioinformatics 2005 Jul 6;21(14):3176-8. Epub 2005 May 6.

Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomédica, Parc Científic de Barcelona Josep Samitier 1-5, Barcelona 08028, Spain.

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http://dx.doi.org/10.1093/bioinformatics/bti486DOI Listing
July 2005

Partition of protein solvation into group contributions from molecular dynamics simulations.

Proteins 2005 Jan;58(1):101-9

Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.

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http://dx.doi.org/10.1002/prot.20292DOI Listing
January 2005

Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?

Proteins 2004 Nov;57(3):458-67

Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica, Barcelona, Spain.

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http://dx.doi.org/10.1002/prot.20169DOI Listing
November 2004

Continuum and discrete calculation of fractional contributions to solvation free energy.

J Comput Chem 2003 Oct;24(13):1610-23

Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain.

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http://dx.doi.org/10.1002/jcc.10323DOI Listing
October 2003

Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad.

J Am Chem Soc 2003 May;125(19):5654-62

Departament de Química Orgànica, Universitat de Barcelona, C/, Martí i Franquès 1-11, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1021/ja0344157DOI Listing
May 2003

Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair.

RNA 2002 May;8(5):659-70

Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis 55455-0431, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370286PMC
http://dx.doi.org/10.1017/s1355838202020277DOI Listing
May 2002