SH3 domain-peptide binding energy calculations based on structural ensemble and multiple peptide templates.

ABSTRACT: SH3 domains mediate signal transduction by recognizing short peptides. Understanding of the driving forces in peptide recognitions will help us to predict the binding specificity of the domain-peptide recognition and to understand the molecular interaction networks of cells. However, accurate calculation of the binding energy is a tough challenge. In this study, we propose three ideas for improving our ability to predict the binding energy between SH3 domains and peptides: (1) utilizing the structural ensembles sampled from a molecular dynamics simulation trajectory, (2) utilizing multiple peptide templates, and (3) optimizing the sequence-structure mapping. We tested these three ideas on ten previously studied SH3 domains for which SPOT analysis data were available. The results indicate t

SUBMITTER: Hong S 

PROVIDER: S-EPMC2939891 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature