ArticleBMC bioinformatics2008
Wanted: unique names for unique atom positions. PDB-wide analysis of diastereotopic atom names of small molecules containing diphosphate.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed, 12 citations in OpenAlex.
- Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR.Magnetic resonance (Gottingen, Germany) · 2023Article
- Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference. Introduction.BMC bioinformatics · 2009Article
- Proceedings of the 2008 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference.BMC bioinformatics · 2008Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundBiological 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.
resultsOf 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.
conclusionThe 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.
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