Predicting transcription factor specificity with all-atom models.

ABSTRACT: The binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expression of a gene. Computational prediction of sites recognized by a TF has traditionally relied upon knowledge of several cognate sites, rather than an ab initio approach. Here, we examine the possibility of using structure-based energy calculations that require no knowledge of bound sites but rather start with the structure of a protein-DNA complex. We study the PurR Escherichia coli TF, and explore to which extent atomistic models of protein-DNA complexes can be used to distinguish between cognate and noncognate DNA sites. Particular emphasis is placed on systematic evaluation of this approach by comparing its performance with bioinformatic methods, by testing it against random decoys and si

SUBMITTER: Rahi SJ 

PROVIDER: S-EPMC2577325 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature