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

Rebecca F. Alford; Andrew Leaver-Fay; Jeliazko R. Jeliazkov; Matthew J. O'Meara; Frank P. DiMaio; Hahnbeom Park; Maxim V. Shapovalov; P. Douglas Renfrew; Vikram K. Mulligan; Kalli Kappel; Jason W. Labonte; Michael S. Pacella; Richard Bonneau; Philip Bradley; Roland L. Dunbrack; Rhiju Das; David Baker; Brian Kuhlman; Tanja Kortemme; Jeffrey J. Gray

doi:10.1021/acs.jctc.7b00125

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

Rebecca F. Alford, Andrew Leaver-Fay, Jeliazko R. Jeliazkov, Matthew J. O'Meara, Frank P. DiMaio, Hahnbeom Park, Maxim V. Shapovalov, P. Douglas Renfrew, Vikram K. Mulligan, Kalli Kappel, Jason W. Labonte, Michael S. Pacella, Richard Bonneau, Philip Bradley, Roland L. Dunbrack, Rhiju Das, David Baker, Brian Kuhlman, Tanja Kortemme, Jeffrey J. Gray

Whiting School of Engineering

Research output: Contribution to journal › Article › peer-review

311 Scopus citations

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.

Original language	English (US)
Pages (from-to)	3031-3048
Number of pages	18
Journal	Journal of Chemical Theory and Computation
Volume	13
Issue number	6
DOIs	https://doi.org/10.1021/acs.jctc.7b00125
State	Published - Jun 13 2017

ASJC Scopus subject areas

Computer Science Applications
Physical and Theoretical Chemistry

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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. (2017). The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design. Journal of Chemical Theory and Computation, 13(6), 3031-3048. https://doi.org/10.1021/acs.jctc.7b00125

Alford, RF, Leaver-Fay, A, Jeliazkov, JR, O'Meara, MJ, DiMaio, FP, Park, H, Shapovalov, MV, Renfrew, PD, Mulligan, VK, Kappel, K, Labonte, JW, Pacella, MS, Bonneau, R, Bradley, P, Dunbrack, RL, Das, R, Baker, D, Kuhlman, B, Kortemme, T & Gray, JJ 2017, 'The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design', Journal of Chemical Theory and Computation, vol. 13, no. 6, pp. 3031-3048. https://doi.org/10.1021/acs.jctc.7b00125

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title = "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design",

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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AU - DiMaio, Frank P.

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AU - Labonte, Jason W.

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AU - Bonneau, Richard

AU - Bradley, Philip

AU - Dunbrack, Roland L.

AU - Das, Rhiju

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AU - Kortemme, Tanja

AU - Gray, Jeffrey J.

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

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