1. The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
- Author
-
Maxim V. Shapovalov, Matthew J. O’Meara, Vikram Khipple Mulligan, Frank DiMaio, Hahnbeom Park, Jeffrey J. Gray, Andrew Leaver-Fay, Richard Bonneau, Michael S. Pacella, David Baker, Rhiju Das, Kalli Kappel, Jason W. Labonte, Tanja Kortemme, Rebecca F. Alford, Brian Kuhlman, Roland L. Dunbrack, Philip Bradley, Jeliazko R. Jeliazkov, and P. Douglas Renfrew
- Subjects
0301 basic medicine ,Molecular model ,Computer science ,Macromolecular Substances ,Protein Conformation ,media_common.quotation_subject ,Static Electricity ,Nanotechnology ,Crystal structure ,Computational biology ,Molecular Dynamics Simulation ,010402 general chemistry ,01 natural sciences ,Force field (chemistry) ,Article ,03 medical and health sciences ,Molecular dynamics ,Protein structure ,HIV Protease ,Physical and Theoretical Chemistry ,Function (engineering) ,media_common ,chemistry.chemical_classification ,Physics ,Protein therapeutics ,Biomolecule ,computer.file_format ,Small molecule ,Amino acid ,0104 chemical sciences ,Computer Science Applications ,030104 developmental biology ,Membrane protein ,chemistry ,Atom (standard) ,Mutation ,Nucleic acid ,Thermodynamics ,Modeling and design ,computer ,Energy (signal processing) ,Macromolecule - 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: amodel parameterized 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, beta_nov15. 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 capabilities from soluble proteins to also include membrane proteins, peptides containing non-canonical amino acids, carbohydrates, nucleic acids, and other macromolecules.
- Published
- 2017
- Full Text
- View/download PDF