ShapeME: A tool and web front-end for de novo discovery of structural motifs underpinning protein-DNA interactions.

ABSTRACT: Determining where transcriptional regulators bind within a genome is paramount to understanding how gene expression is regulated. Historically, position weight matrices (PWMs) have been used to define the binding preferences of DNA binding proteins¹. However, PWMs treat the identity of each base in a sequence as an independent and additive measure of binding preference, which can limit their utility². Models that consider higher order interactions between nearby bases yield greater success in predicting proteins' binding to DNA, but for many proteins there is still substantial room for improvement in predicting and understanding the determinants of proteins' binding to DNA³. In addition to DNA sequence motifs, structural motifs (e.g., a narrow minor groove

SUBMITTER: Schroeder JW 

PROVIDER: S-EPMC11838363 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature