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Nucleic Acids Research 2006 34(Database Issue):D199-D203; doi:10.1093/nar/gkj035
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Nucleic Acids Research, 2006, Vol. 34, Database issue D199-D203
© 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

PPD v1.0—an integrated, web-accessible database of experimentally determined protein pKa values

Christopher P. Toseland, Helen McSparron, Matthew N. Davies and Darren R. Flower*

Edward Jenner Institute for Vaccine Research Compton, Berkshire, RG20 7NN, UK

*To whom correspondence should be addressed. Tel: +44 1635 577954; Fax: +44 1635 577901 577908; Email: darren.flower{at}jenner.ac.uk

Received June 17, 2005. Revised September 15, 2005. Accepted September 26, 2005.

The Protein pKa Database (PPD) v1.0 provides a compendium of protein residue-specific ionization equilibria (pKa values), as collated from the primary literature, in the form of a web-accessible postgreSQL relational database. Ionizable residues play key roles in the molecular mechanisms that underlie many biological phenomena, including protein folding and enzyme catalysis. The PPD serves as a general protein pKa archive and as a source of data that allows for the development and improvement of pKa prediction systems. The database is accessed through an HTML interface, which offers two fast, efficient search methods: an amino acid-based query and a Basic Local Alignment Search Tool search. Entries also give details of experimental techniques and links to other key databases, such as National Center for Biotechnology Information and the Protein Data Bank, providing the user with considerable background information. The database can be found at the following URL: http://www.jenner.ac.uk/PPD.


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