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WeNMR: Structural Biology on the Grid

Journal of Grid Computing volume 10, pages 743–767 (2012)Cite this article

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).

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Author notes

  1. Tsjerk A. Wassenaar

    Present address: Biocomputing Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, AB T2N 1N4, Calgary, Canada

  2. Nuno Loureiro-Ferreira

    Present address: European Grid Infrastructure (EGI), 140 Science Park, 1098 XG, Amsterdam, The Netherlands

  3. Wim F. Vranken

    Present address: Department of Structural Biology, VIB, and Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium

  4. Stefano Dal Pra

    Present address: Istituto Nazionale di Fisica Nucleare, CNAF, 40127, Bologna, Italy

Affiliations

  1. Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands

    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 & Alexandre M. J. J. Bonvin

  2. Magnetic Resonance Center, University of Florence, 50019, Sesto Fiorentino, Italy

    Andrea Giachetti, Lucio Ferella, Antonio Rosato & Ivano Bertini

  3. Centre de RMN à très Hauts Champs, Institut des Sciences Analytiques, Université de Lyon, UMR-5280 CNRS, ENS Lyon, UCB Lyon 1, 5 rue de la Doua, 69100, Villeurbanne, France

    Torsten Herrmann

  4. Institute of Organic Chemistry and Chemical Biology and Biomolecular Magnetic Resonance Center, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany

    Hendrik R. A. Jonker & Harald Schwalbe

  5. Institute of Biophysical Chemistry and Biomolecular Magnetic Resonance Center, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany

    Anurag Bagaria, Victor Jaravine & Peter Güntert

  6. European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK

    Wim F. Vranken

  7. Protein Biophysics/IMM, Radboud University Nijmegen, Geert Grooteplein 26-28, Nijmegen, The Netherlands

    Jurgen F. Doreleijers

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

    Gert Vriend

  9. Department of Biochemistry, School of Biological Sciences, Henry Wellcome Building, University of Leicester, Lancaster Road, Leicester, LE1 9HN, UK

    Geerten W. Vuister

  10. European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D22603, Hamburg, Germany

    Daniel Franke, Alexey Kikhney & Dmitri I. Svergun

  11. Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA, Cambridge, UK

    Rasmus H. Fogh, John Ionides & Ernest D. Laue

  12. UAB “Spronk NMR Consultancy”, Palangos gatvë 4, 01402, Vilnius, Lithuania

    Chris Spronk & Simonas Jurkša

  13. Istituto Nazionale di Fisica Nucleare, Sez. di Padova, 35131, Padova, Italy

    Marco Verlato, Simone Badoer, Stefano Dal Pra, Mirco Mazzucato & Eric Frizziero

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  1. Tsjerk A. Wassenaar
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  36. Alexandre M. J. J. Bonvin
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Corresponding author

Correspondence to Alexandre M. J. J. Bonvin.

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Wassenaar, T.A., van Dijk, M., Loureiro-Ferreira, N. et al. WeNMR: Structural Biology on the Grid. J Grid Computing 10, 743–767 (2012). https://doi.org/10.1007/s10723-012-9246-z

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Keywords

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