Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies.

ABSTRACT:

Background

Knowledge of transcription factor-DNA binding patterns is crucial for understanding gene transcription. Numerous DNA-binding proteins are annotated as transcription factors in the literature, however, for many of them the corresponding DNA-binding motifs remain uncharacterized.

Results

The position weight matrices (PWMs) of transcription factors from different structural classes have been determined using a knowledge-based statistical potential. The scoring function calibrated against crystallographic data on protein-DNA contacts recovered PWMs of various members of widely studied transcription factor families such as p53 and NF-kappaB. Where it was possible, extensive comparison to experimental binding affinity data and other physical models was made. Although th

SUBMITTER: Alamanova D 

PROVIDER: S-EPMC2879287 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature