The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
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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.
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Current AF2 versions do not employ energy functions that seek native-like conformations, unlike Rosetta.
“current versions of AF2 do not use energy functions that seek to identify native-like protein conformations, unlike its competitor Rosetta13”
From The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins (2024) · cites this paper as [13]
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- Authors
- Alford, R. F., Leaver-Fay, A., Jeliazkov, J. R., O’Meara, M. J., DiMaio, F. P., Park, H., Shapovalov, M. V., Renfrew, P. D., Mulligan, V. K., Kappel, K., Labonte, J. W., Pacella, M. S., Bonneau, R., Bradley, P., Dunbrack, R. L., Das, R., Baker, D., Kuhlman, B., Kortemme, T., & Gray, J. J.
- Affiliations
- Johns Hopkins University (US)
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, United States
- University of California, San Francisco (US)
- University of Washington (US)
- Fox Chase Cancer Center (US)
- Simons Foundation (US)
- Stanford University (US)
- Fred Hutch Cancer Center (US)
- Howard Hughes Medical Institute (US)
- University of North Carolina at Chapel Hill (US)
- Corresponding author
- Gray, Jeffrey J.
- ORCID
- Alford, Rebecca F.
- Jeliazkov, Jeliazko R.
- O’Meara, Matthew J.
- DiMaio, Frank P.
- Park, Hahnbeom
- Shapovalov, Maxim V.
- Renfrew, P. Douglas
- Mulligan, Vikram K.
- Kappel, Kalli
- Labonte, Jason W.
- Pacella, Michael S.
- Bonneau, Richard
- Bradley, Philip
- Dunbrack, Roland L.
- Das, Rhiju
- Baker, David
- Kuhlman, Brian
- Kortemme, Tanja
- Gray, Jeffrey J.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2017-05-12
- Volume
- 13
- Issue
- 6
- Pages
- 3031-3048
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- PMC
- PMC5717763
- OpenAlex
- W2606439133
- Cited by
- 1,532
- References
- 121
- Citations by year
- 2026: 214 · 2025: 220 · 2024: 209 · 2023: 189 · 2022: 201 · 2021: 179 · 2020: 153 · 2019: 99 · 2018: 52 · 2017: 15
- FWCI
- 35.67
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc
- Locations
- Journal of Chemical Theory and Computation (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- UNC Libraries
- Funders
- National Cancer Institute (F32-CA189246)
- Hertz Foundation
- National Institute of General Medical Sciences (GM-078221, GM-084453, GM-092802, GM-110089, GM-111819, GM-114961, GM-117189, GM-73141)
- Simons Foundation
- National Science Foundation
- Division of Materials Research (1507736)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- energy function, biomolecular modeling, protein structure prediction, protein design, membrane proteins, unnatural amino acids, carbohydrates, nucleic acids, small molecules, conformational energy, force field parameterization
- MeSH terms
- Mutation, Protein Conformation, Thermodynamics, HIV Protease, Macromolecular Substances, Static Electricity, Molecular Dynamics Simulation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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