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Nucleic Acids Research 2007 35(Database issue):D580-D589; doi:10.1093/nar/gkl836
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Nucleic Acids Research, 2007, Vol. 35, Database issue D580-D589
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions

Emily R. Jefferson, Thomas P. Walsh, Timothy J. Roberts1 and Geoffrey J. Barton*

School of Life Sciences Research, College of Life Sciences, University of Dundee Dow Street, Dundee, DD1 5EH, Scotland, UK 1 School of Computing, University of Dundee Dundee, DD1 4HN, Scotland, UK

*To whom correspondence should be addressed. Tel: +44 01382 385860; Fax: +44 01382 385764; Email: geoff{at}compbio.dundee.ac.uk

Received August 16, 2006. Revised October 4, 2006. Accepted October 6, 2006.

SNAPPI-DB, a high performance database of Structures, iNterfaces and Alignments of Protein–Protein Interactions, and its associated Java Application Programming Interface (API) is described. SNAPPI-DB contains structural data, down to the level of atom co-ordinates, for each structure in the Protein Data Bank (PDB) together with associated data including SCOP, CATH, Pfam, SWISSPROT, InterPro, GO terms, Protein Quaternary Structures (PQS) and secondary structure information. Domain–domain interactions are stored for multiple domain definitions and are classified by their Superfamily/Family pair and interaction interface. Each set of classified domain–domain interactions has an associated multiple structure alignment for each partner. The API facilitates data access via PDB entries, domains and domain–domain interactions. Rapid development, fast database access and the ability to perform advanced queries without the requirement for complex SQL statements are provided via an object oriented database and the Java Data Objects (JDO) API. SNAPPI-DB contains many features which are not available in other databases of structural protein–protein interactions. It has been applied in three studies on the properties of protein–protein interactions and is currently being employed to train a protein–protein interaction predictor and a functional residue predictor. The database, API and manual are available for download at: http://www.compbio.dundee.ac.uk/SNAPPI/downloads.jsp.


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