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PPD


NAR Molecular Biology Database Collection entry number 856
Toseland C.P., McSparron H., Doytchinova I.A., M.N.Davies, and Flower D.R.
Aston Pharmacy School, School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET

Database Description

The Protein pKa Database (PPD) v1.0 provides a compendium of protein residue-specific ionisation 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 database 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 BLAST search. Entries also give details of experimental techniques and links to other key databases, such as NCBI and the Protein Data Bank, providing the user with considerable background information. The database can be found at the following URL: http://www.ddg-pharmfac.net/ppd/PPD/pKahomepage.htm.

Acknowledgements

Initial funding for PPD was provided by GlaxoSmithkline, BBSRC, MRC, and the UK Department of Health.

References



1. Toseland CP, McSparron H, Davies MN, Flower DR. PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D199-203.

2. Davies MN, Toseland CP, Moss DS, Flower DR. Benchmarking pK(a) prediction. BMC Biochem. 2006 7:18.

Subcategory: Protein properties

Go to the abstract in the NAR 2006 Database Issue.
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