Development of a motif-based topology-independent structure comparison method to identify evolutionarily related folds.

ABSTRACT: Structure conservation, functional similarities, and homologous relationships that exist across diverse protein topologies suggest that some regions of the protein fold universe are continuous. However, the current structure classification systems are based on hierarchical organizations, which cannot accommodate structural relationships that span fold definitions. Here, we describe a novel, super-secondary-structure motif-based, topology-independent structure comparison method (SmotifCOMP) that is able to quantitatively identify structural relationships between disparate topologies. The basis of SmotifCOMP is a systematically defined super-secondary-structure motif library whose representative geometries are shown to be saturated in the Protein Data Bank and exhibit a unique distribution w

SUBMITTER: Dybas JM 

PROVIDER: S-EPMC5118133 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature