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

Bioinformatics. 2005 Apr 15;21(8):1721-3. doi: 10.1093/bioinformatics/bti232. Epub 2004 Dec 21.

Abstract

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@ims.u-tokyo.ac.jp.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Graphics
  • Computer Simulation
  • DNA / chemistry*
  • DNA-Binding Proteins / chemistry*
  • Internet*
  • Models, Chemical*
  • Models, Molecular*
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Conformation
  • Surface Properties
  • User-Computer Interface*

Substances

  • DNA-Binding Proteins
  • DNA