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This article is part of the supplement: Proceedings of the Fifth Annual MCBIOS Conference. Systems Biology: Bridging the Omics

Open Access Proceedings

Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate

Christopher A Bottoms and Dong Xu*

Author Affiliations

Department of Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA

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BMC Bioinformatics 2008, 9(Suppl 9):S16  doi:10.1186/1471-2105-9-S9-S16

Published: 12 August 2008

Abstract

Background

Biological chemistry is very stereospecific. Nonetheless, the diastereotopic oxygen atoms of diphosphate-containing molecules in the Protein Data Bank (PDB) are often given names that do not uniquely distinguish them from each other due to the lack of standardization. This issue has largely not been addressed by the protein structure community.

Results

Of 472 diastereotopic atom pairs studied from the PDB, 118 were found to have names that are not uniquely assigned. Among the molecules identified with these inconsistencies were many cofactors of enzymatic processes such as mononucleotides (e.g. ADP, ATP, GTP), dinucleotide cofactors (e.g. FAD, NAD), and coenzyme A. There were no overall trends in naming conventions, though ligand-specific trends were prominent.

Conclusion

The lack of standardized naming conventions for diastereotopic atoms of small molecules has left the ad hoc names assigned to many of these atoms non-unique, which may create problems in data-mining of the PDB. We suggest a naming convention to resolve this issue. The in-house software used in this study is available upon request.

A version of the software used for the analyses described in this paper is available at our web site: http://digbio.missouri.edu/ddan/DDAN.htm webcite.