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BMC Bioinformatics. 2010 Jan 7;11:12. doi: 10.1186/1471-2105-11-12.

SKPDB: a structural database of shikimate pathway enzymes.

Author information

1
CEIS/Departamento de Biologia, Instituto de Biociências, UNESP, Rio Claro, São Paulo, Brasil.

Abstract

BACKGROUND:

The functional and structural characterisation of enzymes that belong to microbial metabolic pathways is very important for structure-based drug design. The main interest in studying shikimate pathway enzymes involves the fact that they are essential for bacteria but do not occur in humans, making them selective targets for design of drugs that do not directly impact humans.

DESCRIPTION:

The ShiKimate Pathway DataBase (SKPDB) is a relational database applied to the study of shikimate pathway enzymes in microorganisms and plants. The current database is updated regularly with the addition of new data; there are currently 8902 enzymes of the shikimate pathway from different sources. The database contains extensive information on each enzyme, including detailed descriptions about sequence, references, and structural and functional studies. All files (primary sequence, atomic coordinates and quality scores) are available for downloading. The modeled structures can be viewed using the Jmol program.

CONCLUSIONS:

The SKPDB provides a large number of structural models to be used in docking simulations, virtual screening initiatives and drug design. It is freely accessible at http://lsbzix.rc.unesp.br/skpdb/.

PMID:
20055992
PMCID:
PMC2824673
DOI:
10.1186/1471-2105-11-12
[Indexed for MEDLINE]
Free PMC Article

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