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J Phys Chem B. 2012 Jul 26;116(29):8494-503. doi: 10.1021/jp212541y. Epub 2012 May 10.

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

Author information

  • 1Department of Chemistry and Biochemistry and Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States.

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 for local structure biasing, all of which assume that the structure of the target sequence is not known. When there are no homologues in the database of structures used for local structure biasing, AWSEM calculations produce structural predictions that are somewhat improved compared with prior works using related approaches. The inclusion of a small number of structures from homologous sequences improves structure prediction only marginally, but when the fragment search is restricted to only homologous sequences, AWSEM can perform high resolution structure prediction and can be used for kinetics and dynamics studies.

PMID:
22545654
[PubMed - indexed for MEDLINE]
PMCID:
PMC3406225
Free PMC Article

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