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Bioinformatics Advance Access published online on December 21, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti232
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Bioinformatics © Oxford University Press 2004; all rights reserved.
Received September 2, 2004
Revised December 8, 2004
Accepted December 15, 2004

Applications note

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

Yuko Tsuchiya 1, Kengo Kinoshita 2*, and Haruki Nakamura 1

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

* To whom correspondence should be addressed.
Kengo Kinoshita, E-mail: kino{at}ims.u-tokyo.ac.jp


  Abstract

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, local curvature and 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/.


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