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Bioinformatics Advance Access originally published online on December 21, 2004
Bioinformatics 2005 21(8):1721-1723; doi:10.1093/bioinformatics/bti232
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces

Yuko Tsuchiya 1, Kengo Kinoshita 1,2,*,{dagger} and Haruki Nakamura 1

1Institute for Protein Research, Osaka University 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
2Structure and Function of Biomolecules PRESTO, JST, 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan

*To whom correspondence should be addressed.

Summary: PreDs is a WWW server that predicts the dsDNA-binding sites on protein molecular surfaces generated from the atomic coordinates in a PDB format. The prediction was done by evaluating the electrostatic potential, the local curvature and the global curvature on the surfaces. Results of the prediction can be interactively checked with our original surface viewer.

Availability: PreDs is available free of charge from http://pre-s.protein.osaka-u.ac.jp/~preds/

Contact: kino{at}ims.u-tokyo.ac.jp


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