Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information.

ABSTRACT: In this work, we analyse the potential for using structural knowledge to improve the detection of the DNA-binding helix-turn-helix (HTH) motif from sequence. Starting from a set of DNA-binding protein structures that include a functional HTH motif and have no apparent sequence similarity to each other, two different libraries of hidden Markov models (HMMs) were built. One library included sequence models of whole DNA-binding domains, which incorporate the HTH motif, the second library included shorter models of 'partial' domains, representing only the fraction of the domain that corresponds to the functionally relevant HTH motif itself. The libraries were scanned against a dataset of protein sequences, some containing the HTH motifs, others not. HMM predictions were compared with the resul

SUBMITTER: Pellegrini-Calace M 

PROVIDER: S-EPMC1079965 | biostudies-literature | 2005

REPOSITORIES: biostudies-literature