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J Chem Theory Comput. 2017 Jun 13;13(6):3031-3048. doi: 10.1021/acs.jctc.7b00125. Epub 2017 May 12.

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.

Author information

1
Department of Chemical and Biomolecular Engineering, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States.
2
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill , 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States.
3
Program in Molecular Biophysics, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States.
4
Department of Pharmaceutical Chemistry, University of California at San Francisco , 1700 Fourth Street, San Francisco, California 94158, United States.
5
Department of Biochemistry, University of Washington , J-Wing, Health Sciences Building, Box 357350, Seattle, Washington 98195, United States.
6
Department of Biochemistry, University of Washington , Molecular Engineering and Sciences, Box 351655, 3946 West Stevens Way NE, Seattle, Washington 98195, United States.
7
Institute for Cancer Research, Fox Chase Cancer Center , 333 Cottman Avenue, Philadelphia, Pennsylvania 19111, United States.
8
Department of Biology, Center for Genomics and Systems Biology, New York University , 100 Washington Square East, New York, New York 10003, United States.
9
Center for Computational Biology, Flatiron Institute, Simons Foundation , 162 Fifth Avenue, New York, New York 10010, United States.
10
Biophysics Program, Stanford University , 450 Serra Mall, Stanford, California 94305, United States.
11
Department of Biomedical Engineering, Johns Hopkins University , 3400 North Charles Street, Baltimore, Maryland 21218, United States.
12
Computational Biology Program, Fred Hutchinson Cancer Research Center , 1100 Fairview Avenue North, Seattle, Washington 98109, United States.
13
Howard Hughes Medical Institute, University of Washington , Seattle, Washington 98195, United States.
14
Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco , San Francisco, California 94158, United States.

Abstract

Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parametrized from small-molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, called the Rosetta Energy Function 2015 (REF15). Applying these concepts, we explain how to use Rosetta energies to identify and analyze the features of biomolecular models. Finally, we discuss the latest advances in the energy function that extend its capabilities from soluble proteins to also include membrane proteins, peptides containing noncanonical amino acids, small molecules, carbohydrates, nucleic acids, and other macromolecules.

PMID:
28430426
PMCID:
PMC5717763
DOI:
10.1021/acs.jctc.7b00125
[Indexed for MEDLINE]
Free PMC Article

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