PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces
- 21 December 2004
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 21 (8) , 1721-1723
- https://doi.org/10.1093/bioinformatics/bti232
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. PreDs is available free of charge from http://pre-s.protein.osaka-u.ac.jp/~preds/ kino@ims.u-tokyo.ac.jp.Keywords
This publication has 6 references indexed in Scilit:
- Structure‐based prediction of DNA‐binding sites on proteins Using the empirical preference of electrostatic potential and the shape of molecular surfacesProteins-Structure Function and Bioinformatics, 2004
- eF-site and PDBjViewer: database and viewer for protein functional sitesBioinformatics, 2004
- The Protein Data BankNucleic Acids Research, 2000
- Electrostatic forces in two lysozymes: Calculations and measurements of histidine pKa valuesBiopolymers, 1992
- Numerical Calculations of Electrostatic Potentials of Protein-Solvent Systems by the Self Consistent Boundary MethodJournal of the Physics Society Japan, 1987
- Solvent-Accessible Surfaces of Proteins and Nucleic AcidsScience, 1983