Using structural motif templates to identify proteins with DNA binding function.

ABSTRACT: This 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 C(alpha) 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 A rmsd was selected that gave

SUBMITTER: Jones S 

PROVIDER: S-EPMC156721 | biostudies-literature | 2003 Jun

REPOSITORIES: biostudies-literature