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

doi:10.1007/s10723-012-9246-z

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Journal of Grid Computing

December 2012, Volume 10, Issue 4, pp 743–767

WeNMR: Structural Biology on the Grid

Authors
Authors and affiliations

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. BonvinEmail author

Open Access

Article

First Online:: 30 November 2012

Received:: 12 December 2011
Accepted:: 18 September 2012

DOI: 10.1007/s10723-012-9246-z

Cite this article as:: Wassenaar, T.A., van Dijk, M., Loureiro-Ferreira, N. et al. J Grid Computing (2012) 10: 743. doi:10.1007/s10723-012-9246-z

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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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
Email author

1.Bijvoet Center for Biomolecular Research, Faculty of ScienceUtrecht UniversityUtrechtThe Netherlands
2.Magnetic Resonance CenterUniversity of FlorenceSesto FiorentinoItaly
3.Centre de RMN à très Hauts Champs, Institut des Sciences AnalytiquesUniversité de LyonVilleurbanneFrance
4.Institute of Organic Chemistry and Chemical Biology and Biomolecular Magnetic Resonance CenterGoethe University FrankfurtFrankfurt am MainGermany
5.Institute of Biophysical Chemistry and Biomolecular Magnetic Resonance CenterGoethe University FrankfurtFrankfurt am MainGermany
6.European Bioinformatics InstituteCambridgeUK
7.Protein Biophysics/IMMRadboud University NijmegenNijmegenThe Netherlands
8.CMBIRadboud University Nijmegen Medical CentreNijmegenThe Netherlands
9.Department of Biochemistry, School of Biological Sciences, Henry Wellcome BuildingUniversity of LeicesterLeicesterUK
10.European Molecular Biology Laboratory, Hamburg OutstationHamburgGermany
11.Department of BiochemistryUniversity of CambridgeCambridgeUK
12.UAB “Spronk NMR Consultancy”VilniusLithuania
13.Istituto Nazionale di Fisica NuclearePadovaItaly
14.Biocomputing Group, Department of Biological SciencesUniversity of CalgaryCalgaryCanada
15.European Grid Infrastructure (EGI)AmsterdamThe Netherlands
16.Department of Structural Biology, VIB, and Structural Biology BrusselsVrije Universiteit BrusselBrusselsBelgium
17.Istituto Nazionale di Fisica NucleareCNAFBolognaItaly

WeNMR: Structural Biology on the Grid

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