Welcome to the GPCRmd project!

First GPCRmd prototype




Check out visualization and analysis for the first GPCRmd prototype! A complete set of simulations for crystallized GPCRs is coming soon.


Main features

GPCRmd consists of a web platform and database enabling the following activities:

  • Deposition/storage of molecular dynamics (MD) data
  • Basic analysis of deposited MD trajectories, including e.g.
    • Progression of model quality and stability (e.g. RMSD analysis)
    • Statistics about ligand-receptor interaction (contact frequencies)
    • Dynamic interaction network using flareplots (powered by R. Fonseca and AJ Venkatakrishan)
    • Receptor dynamics (helix bending, rotation, micro switches)
  • Online visualization of molecular dynamics (visualization technology is powered by NGL viewer and MD server)

Additional features

  • Stable (citable) IDs provided for referencing in publications
  • Database browsing and search facilities for non-experts







Participants

  • Pompeu Fabra University, Jana Selent group
  • Pompeu Fabra University, Gianni de Fabritiis
  • Universitat Autonoma de Barcelona (Spain), Leonardo Pardo, Arnau Cordomi
  • Philipps-Universität Marburg, Peter Kolb and Maria Martí Solano
  • Paul Scherrer Institut (PSI), Xavier Deupi
  • Stockholm University, Jens Carlsson group
  • University of Kopenhagen, David Gloriam group
  • Uppsala University, Hugo Gutiérrez de Terán group
  • Institut für Medizinische Physik und Biophysik, Johanna Tiemann, Ramon Guixà González and Peter Hildebrandt
  • University of Warsaw, Sławomir Filipek group
  • CNR-Institute of Neurosciences, Toni Giorgino
  • Stanford University: Rasmus Fonseca and A. J. Venkatakrishnan
  • VU University Amsterdam: Chris de Graaf and Albert J. Kooistra