GPCRmd uncovers the dynamics of the 3D-GPCRome.
Journal article

GPCRmd uncovers the dynamics of the 3D-GPCRome.

  • Rodríguez-Espigares I Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain.
  • Torrens-Fontanals M Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain.
  • Tiemann JKS Institute of Medical Physics and Biophysics, Charite University Medicine Berlin, Berlin, Germany.
  • Aranda-García D Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain.
  • Ramírez-Anguita JM Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain.
  • Stepniewski TM Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain.
  • Worp N Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain.
  • Varela-Rial A Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Spain.
  • Morales-Pastor A Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain.
  • Medel-Lacruz B Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain.
  • Pándy-Szekeres G Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
  • Mayol E Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
  • Giorgino T Biophysics Institute, National Research Council of Italy, Milan, Italy.
  • Carlsson J Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
  • Deupi X Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), Villigen PSI, Switzerland.
  • Filipek S Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland.
  • Filizola M Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • Gómez-Tamayo JC Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
  • Gonzalez A Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
  • Gutiérrez-de-Terán H Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden.
  • Jiménez-Rosés M Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
  • Jespers W Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden.
  • Kapla J Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
  • Khelashvili G Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA.
  • Kolb P Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany.
  • Latek D Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland.
  • Marti-Solano M Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany.
  • Matricon P Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
  • Matsoukas MT Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
  • Miszta P Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland.
  • Olivella M Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
  • Perez-Benito L Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
  • Provasi D Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • Ríos S Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
  • R Torrecillas I Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
  • Sallander J Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden.
  • Sztyler A Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland.
  • Vasile S Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Uppsala, Sweden.
  • Weinstein H Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA.
  • Zachariae U Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK.
  • Hildebrand PW Institute of Medical Physics and Biophysics, Charite University Medicine Berlin, Berlin, Germany.
  • De Fabritiis G Computational Science Laboratory, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Barcelona, Spain.
  • Sanz F Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain.
  • Gloriam DE Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
  • Cordomi A Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.
  • Guixà-González R Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), Villigen PSI, Switzerland. ramon.guixa@psi.ch.
  • Selent J Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain. jana.selent@upf.edu.
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  • 2020-07-15
Published in:
  • Nature methods. - 2020
English G-protein-coupled receptors (GPCRs) are involved in numerous physiological processes and are the most frequent targets of approved drugs. The explosion in the number of new three-dimensional (3D) molecular structures of GPCRs (3D-GPCRome) over the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. Molecular dynamics (MD) simulations have become a widely established technique for exploring the conformational landscape of proteins at an atomic level. However, the analysis and visualization of MD simulations require efficient storage resources and specialized software. Here we present GPCRmd (http://gpcrmd.org/), an online platform that incorporates web-based visualization capabilities as well as a comprehensive and user-friendly analysis toolbox that allows scientists from different disciplines to visualize, analyze and share GPCR MD data. GPCRmd originates from a community-driven effort to create an open, interactive and standardized database of GPCR MD simulations.
Language
  • English
Open access status
green
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Persistent URL
https://sonar.ch/global/documents/126385
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