Prediction of TF target sites based on atomistic models of protein-DNA complexes.

ABSTRACT:

Background

The specific recognition of genomic cis-regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for modeling TF specific recognition rely on the knowledge of large sets of cognate target sites and consider only the information contained in their primary sequence.

Results

Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex. Our algorithm combines information regarding the direct and indirect readout of DNA into an atomistic statistical model, which is used to estimate the interaction potent

SUBMITTER: Angarica VE 

PROVIDER: S-EPMC2585596 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature