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Journal of Grid Computing

, Volume 10, Issue 4, pp 743–767 | Cite as

WeNMR: Structural Biology on the Grid

  • Tsjerk A. Wassenaar
  • Marc van Dijk
  • Nuno Loureiro-Ferreira
  • Gijs van der Schot
  • Sjoerd J. de Vries
  • Christophe Schmitz
  • Johan van der Zwan
  • Rolf Boelens
  • Andrea Giachetti
  • Lucio Ferella
  • Antonio Rosato
  • Ivano Bertini
  • Torsten Herrmann
  • Hendrik R. A. Jonker
  • Anurag Bagaria
  • Victor Jaravine
  • Peter Güntert
  • Harald Schwalbe
  • Wim F. Vranken
  • Jurgen F. Doreleijers
  • Gert Vriend
  • Geerten W. Vuister
  • Daniel Franke
  • Alexey Kikhney
  • Dmitri I. Svergun
  • Rasmus H. Fogh
  • John Ionides
  • Ernest D. Laue
  • Chris Spronk
  • Simonas Jurkša
  • Marco Verlato
  • Simone Badoer
  • Stefano Dal Pra
  • Mirco Mazzucato
  • Eric Frizziero
  • Alexandre M. J. J. Bonvin
Open Access
Article
First Online:
Received:
Accepted:

Abstract

The WeNMR (http://www.wenmr.eu) project is a European Union funded international effort to streamline and automate analysis of Nuclear Magnetic Resonance (NMR) and Small Angle X-Ray scattering (SAXS) imaging data for atomic and near-atomic resolution molecular structures. Conventional calculation of structure requires the use of various software packages, considerable user expertise and ample computational resources. To facilitate the use of NMR spectroscopy and SAXS in life sciences the WeNMR consortium has established standard computational workflows and services through easy-to-use web interfaces, while still retaining sufficient flexibility to handle more specific requests. Thus far, a number of programs often used in structural biology have been made available through application portals. The implementation of these services, in particular the distribution of calculations to a Grid computing infrastructure, involves a novel mechanism for submission and handling of jobs that is independent of the type of job being run. With over 450 registered users (September 2012), WeNMR is currently the largest Virtual Organization (VO) in life sciences. With its large and worldwide user community, WeNMR has become the first Virtual Research Community officially recognized by the European Grid Infrastructure (EGI).

Keywords

Web portals Nuclear magnetic resonance Small angle x-ray scattering Structural biology  Proteins Virtual research community 
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Copyright information

© The Author(s) 2012

Authors and Affiliations

  • Tsjerk A. Wassenaar
    • 1
    • 14
  • Marc van Dijk
    • 1
  • Nuno Loureiro-Ferreira
    • 1
    • 15
  • Gijs van der Schot
    • 1
  • Sjoerd J. de Vries
    • 1
  • Christophe Schmitz
    • 1
  • Johan van der Zwan
    • 1
  • Rolf Boelens
    • 1
  • Andrea Giachetti
    • 2
  • Lucio Ferella
    • 2
  • Antonio Rosato
    • 2
  • Ivano Bertini
    • 2
  • Torsten Herrmann
    • 3
  • Hendrik R. A. Jonker
    • 4
  • Anurag Bagaria
    • 5
  • Victor Jaravine
    • 5
  • Peter Güntert
    • 5
  • Harald Schwalbe
    • 4
  • Wim F. Vranken
    • 6
    • 16
  • Jurgen F. Doreleijers
    • 7
  • Gert Vriend
    • 8
  • Geerten W. Vuister
    • 9
  • Daniel Franke
    • 10
  • Alexey Kikhney
    • 10
  • Dmitri I. Svergun
    • 10
  • Rasmus H. Fogh
    • 11
  • John Ionides
    • 11
  • Ernest D. Laue
    • 11
  • Chris Spronk
    • 12
  • Simonas Jurkša
    • 12
  • Marco Verlato
    • 13
  • Simone Badoer
    • 13
  • Stefano Dal Pra
    • 13
    • 17
  • Mirco Mazzucato
    • 13
  • Eric Frizziero
    • 13
  • Alexandre M. J. J. Bonvin
    • 1
  1. 1.Bijvoet Center for Biomolecular Research, Faculty of ScienceUtrecht UniversityUtrechtThe Netherlands
  2. 2.Magnetic Resonance CenterUniversity of FlorenceSesto FiorentinoItaly
  3. 3.Centre de RMN à très Hauts Champs, Institut des Sciences AnalytiquesUniversité de LyonVilleurbanneFrance
  4. 4.Institute of Organic Chemistry and Chemical Biology and Biomolecular Magnetic Resonance CenterGoethe University FrankfurtFrankfurt am MainGermany
  5. 5.Institute of Biophysical Chemistry and Biomolecular Magnetic Resonance CenterGoethe University FrankfurtFrankfurt am MainGermany
  6. 6.European Bioinformatics InstituteCambridgeUK
  7. 7.Protein Biophysics/IMMRadboud University NijmegenNijmegenThe Netherlands
  8. 8.CMBIRadboud University Nijmegen Medical CentreNijmegenThe Netherlands
  9. 9.Department of Biochemistry, School of Biological Sciences, Henry Wellcome BuildingUniversity of LeicesterLeicesterUK
  10. 10.European Molecular Biology Laboratory, Hamburg OutstationHamburgGermany
  11. 11.Department of BiochemistryUniversity of CambridgeCambridgeUK
  12. 12.UAB “Spronk NMR Consultancy”VilniusLithuania
  13. 13.Istituto Nazionale di Fisica NuclearePadovaItaly
  14. 14.Biocomputing Group, Department of Biological SciencesUniversity of CalgaryCalgaryCanada
  15. 15.European Grid Infrastructure (EGI)AmsterdamThe Netherlands
  16. 16.Department of Structural Biology, VIB, and Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
  17. 17.Istituto Nazionale di Fisica NucleareCNAFBolognaItaly

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