Nucl._Acids_Res.-2003-Jones-2811-23.pdf (758.01 kB)
Using structural motifs to identify proteins with DNA binding function
journal contribution
posted on 2023-06-08, 06:52 authored by Susan Jones, Jonathan A Barker, Irene Nobeli, Janet M ThorntonThis work describes a method for predicting DNA binding function from structure using 3-dimensional templates. Proteins that bind DNA using small contiguous helix¿turn¿helix (HTH) motifs comprise a significant number of all DNA-binding proteins. A structural template library of seven HTH motifs has been created from non-homologous DNA-binding proteins in the Protein Data Bank. The templates were used to scan complete protein structures using an algorithm that calculated the root mean squared deviation (rmsd) for the optimal superposition of each template on each structure, based on Ca backbone coordinates. Distributions of rmsd values for known HTH-containing proteins (true hits) and non-HTH proteins (false hits) were calculated. A threshold value of 1.6 Å rmsd was selected that gave a true hit rate of 88.4% and a false positive rate of 0.7%. The false positive rate was further reduced to 0.5% by introducing an accessible surface area threshold value of 990 Å2 per HTH motif. The template library and the validated thresholds were used to make predictions for target proteins from a structural genomics project.
History
Publication status
- Published
File Version
- Published version
Journal
Nucleic Acids ResearchISSN
0305-1048External DOI
Issue
11Volume
31Page range
2811-2823Pages
13.0Department 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
2016-11-16Usage metrics
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