| URL: | http://lsbzix.rc.unesp.br/skpdb/ |
| Full name: | ShiKimate Pathway DataBase |
| Description: | A structural database of shikimate pathway enzymes. SKPDB is a relational database of protein structures predicted by comparative modeling. We focused our study in enzymes of the shikimate pathway identified in all genome of microorganisms. The main goal of the present database is to provide structural models to be used in docking simulations and drug design. The SKPDB user interface provides user friendly menus, so that all information can be printed in one step from any standrard web browser. All structure files are available for downloading. The database is organized to allow identification of the metabolic pathway and include other information about the modeled protein such as, sequence, animated gif for the structure, stereochemical quality and details about the modeling procedure. |
| Year founded: | 2010 |
| Last update: | 2009-11-03 |
| Version: | v1.0 |
| Accessibility: |
Accessible
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| Country/Region: | Brazil |
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| University/Institution: | Institute of Biosciences |
| Address: | UNESP, Rio Claro, São Paulo, Brasil |
| City: | Rio Claro |
| Province/State: | São Paulo |
| Country/Region: | Brazil |
| Contact name (PI/Team): | Mário S Palma |
| Contact email (PI/Helpdesk): | rb.psenu.cr@amlapsm |
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SKPDB: a structural database of shikimate pathway enzymes. [PMID: 20055992]
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/. |