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Nucleic Acids Research, 2003, Vol. 31, No. 24 7189-7198
© 2003 Oxford University Press

Article

Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins

Susan Jones*, Hugh P. Shanahan, Helen M. Berman1 and Janet M. Thornton

EMBL—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 1 Department of Chemistry, Rutgers, The State University, Piscataway, NJ, 08855-0939, USA

*To whom correspondence should be addressed. Tel: +44 1223 492543; Fax: +44 1223 494486; Email: suej{at}ebi.ac.uk

A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNA-binding proteins and the development of a method of predicting DNA-binding sites using a single feature of these surface patches. Surface patches and the DNA-binding sites were initially analysed for accessibility, electrostatic potential, residue propensity, hydrophobicity and residue conservation. From this, it was observed that the DNA-binding sites were, in general, amongst the top 10% of patches with the largest positive electrostatic scores. This knowledge led to the development of a prediction method in which patches of surface residues were selected such that they excluded residues with negative electrostatic scores. This method was used to make predictions for a data set of 56 non-homologous DNA-binding proteins. Correct predictions made for 68% of the data set.


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