Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for α/β Proteins.

ABSTRACT: The atomistic associative memory, water mediated, structure and energy model (AAWSEM) is an efficient coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using structural information derived from all-atom simulations of long segments of the protein. For α helical proteins, the accuracy of structure prediction using AAWSEM has been established previously. In this article, we examine the capability of AAWSEM to predict the structure of α/β proteins. We also elaborate on an iterative approach that uses the structures from a first round of AAWSEM simulation as fragment memories. This iterative scheme improves the quality of the structure prediction and makes the free energy profile more funneled toward native configurations. W

SUBMITTER: Chen M 

PROVIDER: S-EPMC5398943 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature