Nucl._Acids_Res.-2003-Jones-7189-98.pdf (388.11 kB)
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins
journal contribution
posted on 2023-06-07, 19:38 authored by Susan Jones, Hugh P Shanahan, Helen M Berman, Janet M ThorntonA 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.
History
Publication status
- Published
File Version
- Published version
Journal
Nucleic Acids ResearchISSN
0305-1048External DOI
Issue
24Volume
31Page range
7189-7198Pages
10.0Department affiliated with
- Biochemistry Publications
Notes
Wrote algorithm, conducted analysis and was corresponding authorFull text available
- Yes
Peer reviewed?
- Yes
Legacy Posted Date
2012-02-06First Open Access (FOA) Date
2016-03-22First Compliant Deposit (FCD) Date
2017-03-07Usage metrics
Categories
No categories selectedKeywords
Licence
Exports
RefWorks
BibTeX
Ref. manager
Endnote
DataCite
NLM
DC