Research Article

The CCPN data model for NMR spectroscopy: Development of a software pipeline

  1. Wim F. Vranken1,
  2. Wayne Boucher2,
  3. Tim J. Stevens2,
  4. Rasmus H. Fogh2,
  5. Anne Pajon1,
  6. Miguel Llinas3,
  7. Eldon L. Ulrich4,
  8. John L. Markley4,
  9. John Ionides1,
  10. Ernest D. Laue2,*

Article first published online: 6 APR 2005

DOI: 10.1002/prot.20449

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Volume 59, Issue 4, pages 687–696, 1 June 2005

Additional Information

How to Cite

Vranken, W. F., Boucher, W., Stevens, T. J., Fogh, R. H., Pajon, A., Llinas, M., Ulrich, E. L., Markley, J. L., Ionides, J. and Laue, E. D. (2005), The CCPN data model for NMR spectroscopy: Development of a software pipeline. Proteins: Structure, Function, and Bioinformatics, 59: 687–696. doi: 10.1002/prot.20449

Author Information

  1. 1

    Macromolecular Structure Database, European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom

  2. 2

    Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom

  3. 3

    Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania

  4. 4

    BioMagResBank, University of Wisconsin, Madison, Wisconsin

*Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK

Publication History

  1. Issue published online: 3 MAY 2005
  2. Article first published online: 6 APR 2005
  3. Manuscript Accepted: 9 DEC 2004
  4. Manuscript Received: 4 OCT 2004

Funded by

  • EU. Grant Number: QLG2-CT-2000-01313
  • EC. Grant Number: QLRI-CT-2001-00015
  • BBSRC
  • National Institutes of Health. Grant Numbers: P41 LM005799, GM67965

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Keywords:

  • data model, nuclear magnetic resonance, CcpNmr applications;
  • format conversion;
  • software;
  • high throughput

Abstract

To address data management and data exchange problems in the nuclear magnetic resonance (NMR) community, the Collaborative Computing Project for the NMR community (CCPN) created a “Data Model” that describes all the different types of information needed in an NMR structural study, from molecular structure and NMR parameters to coordinates. This paper describes the development of a set of software applications that use the Data Model and its associated libraries, thus validating the approach. These applications are freely available and provide a pipeline for high-throughput analysis of NMR data. Three programs work directly with the Data Model: CcpNmr Analysis, an entirely new analysis and interactive display program, the CcpNmr FormatConverter, which allows transfer of data from programs commonly used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment (Carnegie Mellon University), which was rewritten to interact directly with the Data Model. The ARIA 2.0 software for structure calculation (Institut Pasteur) and the QUEEN program for validation of restraints (University of Nijmegen) were extended to provide conversion of their data to the Data Model. During these developments the Data Model has been thoroughly tested and used, demonstrating that applications can successfully exchange data via the Data Model. The software architecture developed by CCPN is now ready for new developments, such as integration with additional software applications and extensions of the Data Model into other areas of research. Proteins 2005. © 2005 Wiley-Liss, Inc.

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