Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 13, Issue 6, Pages 3031-3048Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.7b00125
Keywords
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Funding
- Hertz Foundation Fellowship
- NSF Graduate Research Fellowship
- NIH [GM-078221, GM-73141, GM-084453, GM-111819, F32-CA189246, GM-092802, GM-110089, GM-117189]
- NSF [GM-114961]
- Simons Foundation
- NSF BMAT [1507736]
- SGF Galiban Fellowship
- Division Of Materials Research
- Direct For Mathematical & Physical Scien [1507736] Funding Source: National Science Foundation
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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.
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