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Nucleic Acids Research 2006 34(Database Issue):D306-D309; doi:10.1093/nar/gkj105
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Nucleic Acids Research, 2006, Vol. 34, Database issue D306-D309
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

The PMDB Protein Model Database

Tiziana Castrignanò, Paolo D'Onorio De Meo, Domenico Cozzetto1, Ivano Giuseppe Talamo1 and Anna Tramontano1,2,*

CASPUR, Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca Via dei Tizii, 6/b, I-00185 Rome, Italy 1Department of Biochemical Sciences, University ‘La Sapienza’ P.le Aldo Moro, 5, I-00185 Rome, Italy 2Istituto Pasteur—Fondazione Cenci Bolognetti, University ‘La Sapienza’ P.le Aldo Moro, 5, I-00185 Rome, Italy

*To whom correspondence should be addressed. Tel: +39 0649910556; Fax: +39 0649910717; Email: anna.tramontano{at}uniroma1.it

Received July 28, 2005. Revised October 17, 2005. Accepted October 17, 2005.

The Protein Model Database (PMDB) is a public resource aimed at storing manually built 3D models of proteins. The database is designed to provide access to models published in the scientific literature, together with validating experimental data. It is a relational database and it currently contains >74 000 models for ~240 proteins. The system is accessible at http://www.caspur.it/PMDB and allows predictors to submit models along with related supporting evidence and users to download them through a simple and intuitive interface. Users can navigate in the database and retrieve models referring to the same target protein or to different regions of the same protein. Each model is assigned a unique identifier that allows interested users to directly access the data.


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