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

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

Research output: Contribution to journalArticle

Abstract

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.
Original languageEnglish
Pages (from-to)D199-D203
Number of pages5
JournalNucleic Acids Research
Volume34
Issue numberSuppl.1
DOIs
Publication statusPublished - Jan 2006

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© The Author 2006. Published by Oxford University Press. All rights reserved
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