PiDNA: Predicting protein-DNA interactions with structural models.

ABSTRACT: Predicting binding sites of a transcription factor in the genome is an important, but challenging, issue in studying gene regulation. In the past decade, a large number of protein-DNA co-crystallized structures available in the Protein Data Bank have facilitated the understanding of interacting mechanisms between transcription factors and their binding sites. Recent studies have shown that both physics-based and knowledge-based potential functions can be applied to protein-DNA complex structures to deliver position weight matrices (PWMs) that are consistent with the experimental data. To further use the available structural models, the proposed Web server, PiDNA, aims at first constructing reliable PWMs by applying an atomic-level knowledge-based scoring function on numerous in silico muta

SUBMITTER: Lin CK 

PROVIDER: S-EPMC3692134 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature