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

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


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 55:483â??186, 2004; Nederveen et al. in Proteins 59:662â??672, 2005; Saccenti and Rosato in J Biomol NMR 40:251â??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 42:376â??384, 2009; Sanderson in Nature 459:1038â??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 â??cleanedâ?? 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.

• Content Type Journal Article
• Pages 389-396
• DOI 10.1007/s10858-009-9378-z
• Authors
  • Jurgen F. Doreleijers, Radboud University Medical Centre Nijmegen Centre for Molecular and Biomolecular Informatics Geert Grooteplein 26-28 PO Box 9101 6500 HB Nijmegen The Netherlands
  • Wim F. Vranken, European Bioinformatics Institute Protein Data Bank in Europe Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD UK
  • Christopher Schulte, University of Wisconsin-Madison BioMagResBank, Department of Biochemistry 433 Babcock Dr. Madison WI 53706 USA
  • Jundong Lin, University of Wisconsin-Madison BioMagResBank, Department of Biochemistry 433 Babcock Dr. Madison WI 53706 USA
  • Jonathan R. Wedell, University of Wisconsin-Madison BioMagResBank, Department of Biochemistry 433 Babcock Dr. Madison WI 53706 USA
  • Christopher J. Penkett, European Bioinformatics Institute Protein Data Bank in Europe Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD UK
  • Geerten W. Vuister, Radboud University Medical Centre Nijmegen Protein Biophysics/IMM Geert Grooteplein 26-28 PO Box 9101 6500 HB Nijmegen The Netherlands
  • Gert Vriend, Radboud University Medical Centre Nijmegen Centre for Molecular and Biomolecular Informatics Geert Grooteplein 26-28 PO Box 9101 6500 HB Nijmegen The Netherlands
  • John L. Markley, University of Wisconsin-Madison BioMagResBank, Department of Biochemistry 433 Babcock Dr. Madison WI 53706 USA
  • Eldon L. Ulrich, University of Wisconsin-Madison BioMagResBank, Department of Biochemistry 433 Babcock Dr. Madison WI 53706 USA

• • Journal Journal of Biomolecular NMR
  • Online ISSN 1573-5001
  • Print ISSN 0925-2738
  • Journal Volume Volume 45
  • Journal Issue Volume 45, Number 4

Source: Journal of Biomolecular NMR