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

Jones, Susan, Shanahan, Hugh P, Berman, Helen M and Thornton, Janet M (2003) Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Research, 31 (24). pp. 7189-7198. ISSN 0305-1048

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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.

Item Type: Article
Additional Information: Wrote algorithm, conducted analysis and was corresponding author
Schools and Departments: School of Life Sciences > Biochemistry
Depositing User: Sue Jones
Date Deposited: 06 Feb 2012 18:20
Last Modified: 07 Mar 2017 09:08
URI: http://sro.sussex.ac.uk/id/eprint/15829

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