The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries.

TitleThe NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries.
Publication TypeJournal Article
Year of Publication2009
AuthorsDoreleijers, J. F., W. F. Vranken, C. Schulte, J. Lin, J. R. Wedell, C. J. Penkett, G. W. Vuister, G. Vriend, J. L. Markley, and E. L. Ulrich
JournalJ Biomol NMR
Volume45
Issue4
Pagination389-96
Date Published2009 Dec
ISSN1573-5001
KeywordsAutomatic Data Processing, Databases, Protein, Humans, Nuclear Magnetic Resonance, Biomolecular, Nucleic Acids, Proteins, Reference Standards, Software
Abstract

Several pilot experiments have indicated that improvements in older NMR structures can be expected by applying modern software and new protocols (Nabuurs et al. in Proteins 55:483-186, 2004; Nederveen et al. in Proteins 59:662-672, 2005; Saccenti and Rosato in J Biomol NMR 40:251-261, 2008). A recent large scale X-ray study also has shown that modern software can significantly improve the quality of X-ray structures that were deposited more than a few years ago (Joosten et al. in J. Appl Crystallogr 42:376-384, 2009; Sanderson in Nature 459:1038-1039, 2009). Recalculation of three-dimensional coordinates requires that the original experimental data are available and complete, and are semantically and syntactically correct, or are at least correct enough to be reconstructed. For multiple reasons, including a lack of standards, the heterogeneity of the experimental data and the many NMR experiment types, it has not been practical to parse a large proportion of the originally deposited NMR experimental data files related to protein NMR structures. This has made impractical the automatic recalculation, and thus improvement, of the three dimensional coordinates of these structures. We here describe a large-scale international collaborative effort to make all deposited experimental NMR data semantically and syntactically homogeneous, and thus useful for further research. A total of 4,014 out of 5,266 entries were 'cleaned' in this process. For 1,387 entries, human intervention was needed. Continuous efforts in automating the parsing of both old, and newly deposited files is steadily decreasing this fraction. The cleaned data files are available from the NMR restraints grid at http://restraintsgrid.bmrb.wisc.edu .

DOI10.1007/s10858-009-9378-z
Alternate JournalJ. Biomol. NMR
PubMed ID19809795
PubMed Central IDPMC2777234
Grant ListBB/E007511/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom
P41 LM005799 / LM / NLM NIH HHS / United States
P41 LM05799 / LM / NLM NIH HHS / United States
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