title: Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.
abstract: 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.
authors.affiliation: EMBL--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. suej@ebi.ac.uk
authors.forename: Susan
authors.initials: S
authors.lastname: Jones
authors.forename: Hugh P
authors.initials: HP
authors.lastname: Shanahan
authors.forename: Helen M
authors.initials: HM
authors.lastname: Berman
authors.forename: Janet M
authors.initials: JM
authors.lastname: Thornton
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D030541:Databases, Genetic; D057927:Hydrophobic and Hydrophilic Interactions; D055672:Static Electricity
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA