DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions.

ABSTRACT: The structures of DNA-protein complexes have illuminated the diversity of DNA-protein binding mechanisms shown by different protein families. This lack of generality could pose a great challenge for predicting DNA-protein interactions. To address this issue, we have developed a knowledge-based method, DNA-binding Domain Hunter (DBD-Hunter), for identifying DNA-binding proteins and associated binding sites. The method combines structural comparison and the evaluation of a statistical potential, which we derive to describe interactions between DNA base pairs and protein residues. We demonstrate that DBD-Hunter is an accurate method for predicting DNA-binding function of proteins, and that DNA-binding protein residues can be reliably inferred from the corresponding templates if identified. In

SUBMITTER: Gao M 

PROVIDER: S-EPMC2475642 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature