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Open Access Database

SKPDB: a structural database of shikimate pathway enzymes

Helen A Arcuri1, Geraldo FD Zafalon2, Evandro A Marucci2, Carlos E Bonalumi2, Nelson JF da Silveira3, José M Machado2, Walter F de Azevedo4* and Mário S Palma1*

Author Affiliations

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

2 Departamento de Ciência da Computação e Estatística, UNESP/IBILCE, São José do Rio Preto, São Paulo, Brasil

3 Departamento de Ciências Exatas, UNIFAL, Alfenas, Minas Gerais, Brasil

4 Faculdade de Biociências, PUCRS, Porto Alegre, Rio Grande do Sul, Brasil

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BMC Bioinformatics 2010, 11:12  doi:10.1186/1471-2105-11-12

Published: 7 January 2010

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/ webcite.