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

被引：879

作者：

Alford, Rebecca F. ^{[1
]}

Leaver-Fay, Andrew ^{[2
]}

Jeliazkov, Jeliazko R. ^{[3
]}

O'Meara, Matthew J. ^{[4
]}

DiMaio, Frank P. ^{[5
]}

Park, Hahnbeom ^{[6
]}

Shapovalov, Maxim V. ^{[7
]}

Renfrew, P. Douglas ^{[8
,9
]}

Mulligan, Vikram K. ^{[6
]}

Kappel, Kalli ^{[10
]}

Labonte, Jason W. ^{[1
]}

Pacella, Michael S. ^{[11
]}

Bonneau, Richard ^{[8
,13
]}

Bradley, Philip ^{[12
]}

Dunbrack, Roland L., Jr. ^{[7
]}

Das, Rhiju ^{[10
]}

Baker, David ^{[6
,14
]}

Kuhlman, Brian ^{[2
]}

Kortemme, Tanja ^{[13
]}

Gray, Jeffrey J. ^{[1
,3
]}

机构：

[1] Johns Hopkins Univ, Dept Chem & Biomol Engn, 3400 North Charles St, Baltimore, MD 21218 USA

[2] Univ North Carolina Chapel Hill, Dept Biochem & Biophys, 120 Mason Farm Rd, Chapel Hill, NC 27599 USA

[3] Johns Hopkins Univ, Program Mol Biophys, 3400 North Charles St, Baltimore, MD 21218 USA

[4] Univ Calif San Francisco, Dept Pharmaceut Chem, 1700 Fourth St, San Francisco, CA 94158 USA

[5] Univ Washington, Dept Biochem, J Wing,Hlth Sci Bldg,Box 357350, Seattle, WA 98195 USA

[6] Univ Washington, Dept Biochem, Mol Engn & Sci, Box 351655,3946 West Stevens Way NE, Seattle, WA 98195 USA

[7] Fox Chase Canc Ctr, Inst Canc Res, 333 Cottman Ave, Philadelphia, PA 19111 USA

[8] NYU, Dept Biol, Ctr Genom & Syst Biol, 100 Washington Sq East, New York, NY 10003 USA

[9] Simons Fdn, Flatiron Inst, Ctr Computat Biol, 162 Fifth Ave, New York, NY 10010 USA

[10] Stanford Univ, Biophys Program, 450 Serra Mall, Stanford, CA 94305 USA

[11] Johns Hopkins Univ, Dept Biomed Engn, 3400 North Charles St, Baltimore, MD 21218 USA

[12] Fred Hutchinson Canc Res Ctr, Computat Biol Program, 1100 Fairview Ave North, Seattle, WA 98109 USA

[13] Univ Calif San Francisco, Dept Bioengn & Therapeut Sci, San Francisco, CA 94158 USA

[14] Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA

来源：

JOURNAL OF CHEMICAL THEORY AND COMPUTATION | 2017年 / 13卷 / 06期

基金：

美国国家科学基金会;

关键词：

PROTEIN-PROTEIN DOCKING; NOVO STRUCTURE PREDICTION; CONSISTENT FORCE-FIELD; SIMPLE PHYSICAL MODEL; SIMULTANEOUS-OPTIMIZATION; COMPUTATIONAL DESIGN; MOLECULAR-FIELDS; ROTAMER LIBRARY; LIGAND DOCKING; SHORT-RANGE;

D O I：

10.1021/acs.jctc.7b00125

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

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.

引用

页码：3031 / 3048

页数：18

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