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. 2019 Sep 15;35(18):3510-3511.
doi: 10.1093/bioinformatics/btz115.

Finding enzyme cofactors in Protein Data Bank

Abhik Mukhopadhyay  1 , Neera Borkakoti  1 , Lukáš Pravda  1 , Jonathan D Tyzack  1 , Janet M Thornton  1 , Sameer Velankar  1
Affiliations

Finding enzyme cofactors in Protein Data Bank

Abhik Mukhopadhyay et al. Bioinformatics. .

Abstract

Motivation: Cofactors are essential for many enzyme reactions. The Protein Data Bank (PDB) contains >67 000 entries containing enzyme structures, many with bound cofactor or cofactor-like molecules. This work aims to identify and categorize these small molecules in the PDB and make it easier to find them.

Results: The Protein Data Bank in Europe (PDBe; pdbe.org) has implemented a pipeline to identify enzyme cofactor and cofactor-like molecules, which are now part of the PDBe weekly release process.

Availability and implementation: Information is made available on the individual PDBe entry pages at pdbe.org and programmatically through the PDBe REST API (pdbe.org/api).

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
The steps implemented to identify new bound molecules that are cofactor or cofactor like
See this image and copyright information in PMC

References

    1. Dana J.M., et al. (2019) SIFTS: updated structure integration with function, taxonomy and sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. Nucleic Acids Res. ,47, D482–D489. - PMC - PubMed
    1. Fischer J.D., et al. (2010) The cofactor database: organic cofactors in enzyme catalysis. Bioinformatics ,26, 2496–2497. - PMC - PubMed
    1. Mir S., et al. (2018) PDBe: towards reusable data delivery infrastructure at protein data bank in europe. Nucleic Acids Res. ,46, D486–D492. - PMC - PubMed
    1. Placzek S., et al. (2017) BRENDA in 2017: new perspectives and new tools in BRENDA. Nucleic Acids Res. ,45, D380–D388. - PMC - PubMed
    1. Sehnal D., et al. (2012) SiteBinder: an improved approach for comparing multiple protein structural motifs. J. Chem. Inf. Model. ,52, 343–359. - PubMed

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