Straightforward and complete deposition of NMR data to the PDBe.

TitleStraightforward and complete deposition of NMR data to the PDBe.
Publication TypeJournal Article
Year of Publication2010
AuthorsPenkett, C. J., G. van Ginkel, S. Velankar, J. G Swaminathan, E. L. Ulrich, S. Mading, T. J. Stevens, R. H. Fogh, A. Gutmanas, G. J. Kleywegt, K. Henrick, and W. F. Vranken
JournalJ Biomol NMR
Volume48
Issue2
Pagination85-92
Date Published2010 Oct
ISSN1573-5001
KeywordsDatabase Management Systems, Databases, Protein, Nuclear Magnetic Resonance, Biomolecular, Proteins, User-Computer Interface
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 .

DOI10.1007/s10858-010-9439-3
Alternate JournalJ. Biomol. NMR
PubMed ID20680401
PubMed Central IDPMC2950272
Grant List088944 / / Wellcome Trust / United Kingdom
B20259 / / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/E005071/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/E007511/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
BB/H004130/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
BBE007511 / / Biotechnology and Biological Sciences Research Council / United Kingdom
LM05799 / LM / NLM NIH HHS / United States
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