A modular perspective of protein structures: application to fragment based loop modeling.

ABSTRACT: Proteins can be decomposed into supersecondary structure modules. We used a generic definition of supersecondary structure elements, so-called Smotifs, which are composed of two flanking regular secondary structures connected by a loop, to explore the evolution and current variety of structure building blocks. Here, we discuss recent observations about the saturation of Smotif geometries in protein structures and how it opens new avenues in protein structure modeling and design. As a first application of these observations we describe our loop conformation modeling algorithm, ArchPred that takes advantage of Smotifs classification. In this application, instead of focusing on specific loop properties the method narrows down possible template conformations in other, often not homologous stru

SUBMITTER: Fernandez-Fuentes N 

PROVIDER: S-EPMC3635063 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature