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

Cancer Signaling and Microenvironment (CSM)

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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.

Original language	English
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

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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

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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.",

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

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doi = "10.1021/acs.jctc.7b00125",

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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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AU - Leaver-Fay, Andrew

AU - Jeliazkov, Jeliazko R.

AU - O'Meara, Matthew J.

AU - DiMaio, Frank P.

AU - Park, Hahnbeom

AU - Shapovalov, Maxim V.

AU - Renfrew, P. Douglas

AU - Mulligan, Vikram K.

AU - Kappel, Kalli

AU - Labonte, Jason W.

AU - Pacella, Michael S.

AU - Bonneau, Richard

AU - Bradley, Philip

AU - Dunbrack, Roland L.

AU - Das, Rhiju

AU - Baker, David

AU - Kuhlman, Brian

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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