Sharing DNA-binding information across structurally similar proteins enables accurate specificity determination.

ABSTRACT: We are now in an era where protein-DNA interactions have been experimentally assayed for thousands of DNA-binding proteins. In order to infer DNA-binding specificities from these data, numerous sophisticated computational methods have been developed. These approaches typically infer DNA-binding specificities by considering interactions for each protein independently, ignoring related and potentially valuable interaction information across other proteins that bind DNA via the same structural domain. Here we introduce a framework for inferring DNA-binding specificities by considering protein-DNA interactions for entire groups of structurally similar proteins simultaneously. We devise both constrained optimization and label propagation algorithms for this task, each balancing observations at

SUBMITTER: Wetzel JL 

PROVIDER: S-EPMC7028011 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature