AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing.

ABSTRACT: The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained protein force field. AWSEM contains physically motivated terms, such as hydrogen bonding, as well as a bioinformatically based local structure biasing term, which efficiently takes into account many-body effects that are modulated by the local sequence. When combined with appropriate local or global alignments to choose memories, AWSEM can be used to perform de novo protein structure prediction. Herein we present structure prediction results for a particular choice of local sequence alignment method based on short residue sequences called fragments. We demonstrate the model's structure prediction capabilities for three levels of global homology between the target sequence and those proteins used

SUBMITTER: Davtyan A 

PROVIDER: S-EPMC3406225 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature