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

Susan Jones, Hugh P. Shanahan, Helen M. Berman, Janet M. Thornton

Research output: Contribution to journalArticlepeer-review

156 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)7189-7198
Number of pages10
JournalNucleic acids research
Issue number24
StatePublished - Dec 15 2003

All Science Journal Classification (ASJC) codes

  • Genetics


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