SKPDB: a structural database of shikimate pathway enzymes

BMC Bioinformatics

Database

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

[1] CEIS/Departamento de Biologia, Instituto de Biociências, UNESP, Rio Claro, São Paulo, Brasil;Departamento de Ciência da Computação e Estatística, UNESP/IBILCE, São José do Rio Preto, São Paulo, Brasil;Departamento de Ciências Exatas, UNIFAL, Alfenas, Minas Gerais, Brasil;Faculdade de Biociências, PUCRS, Porto Alegre, Rio Grande do Sul, Brasil;

关键词: Root Mean Square Deviation;    Shikimate Pathway;    External Link;    Root Mean Square Deviation;    Erythrose;   

DOI  :  10.1186/1471-2105-11-12

 received in 2009-05-12, accepted in 2010-01-07,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundThe functional and s tructural 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.DescriptionThe 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.ConclusionsThe 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/.

【 授权许可】

Unknown   
© Arcuri et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.