Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields.

ABSTRACT: When good structural templates can be identified, template-based modeling is the most reliable way to predict the tertiary structure of proteins. In this study, we combine template-based modeling with a realistic coarse-grained force field, AWSEM, that has been optimized using the principles of energy landscape theory. The Associative memory, Water mediated, Structure and Energy Model (AWSEM) is a coarse-grained force field having both transferable tertiary interactions and knowledge-based local-in-sequence interaction terms. We incorporate template information into AWSEM by introducing soft collective biases to the template structures, resulting in a model that we call AWSEM-Template. Structure prediction tests on eight targets, four of which are in the low sequence identity "twilight zon

SUBMITTER: Chen M 

PROVIDER: S-EPMC6713208 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature