SKPDB: a structural database of shikimate pathway enzymes

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 t...

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Bibliographic Details
Published in:BMC bioinformatics 2010-01, Vol.11 (1), p.12-12, Article 12
Main Authors: Arcuri, Helen A, Zafalon, Geraldo Fd, Marucci, Evandro A, Bonalumi, Carlos E, da Silveira, Nelson Jf, Machado, José M, de Azevedo, Jr, Walter F, Palma, Mário S
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Computational Biology
Databases, Protein
Enzymes
Enzymes - chemistry
Online databases
Physiological aspects
Protein Conformation
Sequence Analysis, Protein
Shikimic Acid - metabolism
Software
Structure
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Summary: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. 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. 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/.
ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-11-12