PairK: Pairwise k-mer alignment for quantifying protein motif conservation in disordered regions.

ABSTRACT: Protein-protein interactions are often mediated by a modular peptide recognition domain binding to a short linear motif (SLiM) in the disordered region of another protein. The ability to predict domain-SLiM interactions would allow researchers to map protein interaction networks, predict the effects of perturbations to those networks, and develop biologically meaningful hypotheses. Unfortunately, sequence database searches for SLiMs generally yield mostly biologically irrelevant motif matches or false positives. To improve the prediction of novel SLiM interactions, researchers employ filters to discriminate between biologically relevant and improbable motif matches. One promising criterion for identifying biologically relevant SLiMs is the sequence conservation of the motif, exploiting the

SUBMITTER: Halpin JC 

PROVIDER: S-EPMC11291154 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature