Straightforward and complete deposition of NMR data to the PDBe

[nmrlearner]

Abstract We present a suite of software for the complete and easy deposition of NMR data to the PDB and BMRB. This suite uses the CCPN framework and introduces a freely downloadable, graphical desktop application called CcpNmr Entry Completion Interface (ECI) for the secure editing of experimental information and associated datasets through the lifetime of an NMR project. CCPN projects can be created within the CcpNmr Analysis software or by importing existing NMR data files using the CcpNmr FormatConverter. After further data entry and checking with the ECI, the project can then be rapidly deposited to the PDBe using AutoDep, or exported as a complete deposition NMR-STAR file. In full CCPN projects created with ECI, it is straightforward to select chemical shift lists, restraint data sets, structural ensembles and all relevant associated experimental collection details, which all are or will become mandatory when depositing to the PDB. Instructions and download information for the ECI are available from the PDBe web site at http://www.ebi.ac.uk/pdbe/nmr/deposition/eci.html.

• Content Type Journal Article
• DOI 10.1007/s10858-010-9439-3
• Authors
  • Christopher J. Penkett, European Bioinformatics Institute Protein Data Bank in Europe Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK
  • Glen van Ginkel, European Bioinformatics Institute Protein Data Bank in Europe Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK
  • Sameer Velankar, European Bioinformatics Institute Protein Data Bank in Europe Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK
  • Jawahar Swaminathan, European Bioinformatics Institute Protein Data Bank in Europe Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK
  • Eldon L. Ulrich, University of Wisconsin Madison BioMagResBank, Department of Biochemistry 433 Babcock Dr. Madison WI 53706 USA
  • Steve Mading, University of Wisconsin Madison BioMagResBank, Department of Biochemistry 433 Babcock Dr. Madison WI 53706 USA
  • Tim J. Stevens, University of Cambridge Department of Biochemistry 80 Tennis Court Road Cambridge CB2 1GA UK
  • Rasmus H. Fogh, University of Cambridge Department of Biochemistry 80 Tennis Court Road Cambridge CB2 1GA UK
  • Aleksandras Gutmanas, European Bioinformatics Institute Protein Data Bank in Europe Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK
  • Gerard J. Kleywegt, European Bioinformatics Institute Protein Data Bank in Europe Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK
  • Kim Henrick, European Bioinformatics Institute Protein Data Bank in Europe Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK
  • Wim F. Vranken, European Bioinformatics Institute Protein Data Bank in Europe Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK

• • Journal Journal of Biomolecular NMR
  • Online ISSN 1573-5001
  • Print ISSN 0925-2738

Source: Journal of Biomolecular NMR