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Bioinformatics Advance Access originally published online on April 8, 2009
Bioinformatics 2009 25(12):1559-1560; doi:10.1093/bioinformatics/btp243
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

BIPA: a database for protein–nucleic acid interaction in 3D structures

Semin Lee * and Tom L Blundell

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Old Addenbrooke's Site, Cambridge CB2 1GA, UK

*To whom correspondence should be addressed.


  Abstract

Summary:BIPA is a database for protein–nucleic acid interactions in 3D structures. The database provides various physicochemical features of protein–nucleic acid interface such as size, shape, residue propensity, secondary structure composition and intermolecular interactions. The database also contains multiple structural alignments of nucleic acid-binding protein families with annotations of local environments in order to allow definition of features that influence acceptability of mutations at a particular position in a protein family. A web interface has been designed to present the results of these analyses and facilitate navigation of protein–nucleic acid interfaces.

Availability: http://www-cryst.bioc.cam.ac.uk/bipa

Contact:semin{at}cryst.bioc.cam.ac.uk

Supplementary information:Supplementary data are available at Bioinformatics online.

Associate Editor: Anna Tramontano

Received on February 24, 2009; revised on April 5, 2009; accepted on April 5, 2009

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