The Rosetta all-atom energy function for macromolecular modeling and design
Rebecca F. Alford,
Jeliazko R. Jeliazkov,
Matthew J. O'Meara,
Frank P DiMaio,
Maxim V Shapovalov,
P. Douglas Renfrew,
Vikram K Mulligan,
Jason W. Labonte,
Michael S Pacella,
Roland L. Dunbrack,
Jeffrey J. Gray
Posted 07 Feb 2017
bioRxiv DOI: 10.1101/106054 (published DOI: 10.1021/acs.jctc.7b00125)
Posted 07 Feb 2017
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 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, Aasgard2017. 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.
- Downloaded 2,850 times
- Download rankings, all-time:
- Site-wide: 2,158 out of 94,912
- In biophysics: 53 out of 4,144
- Year to date:
- Site-wide: 44,099 out of 94,912
- Since beginning of last month:
- Site-wide: 42,515 out of 94,912
Downloads over time
Distribution of downloads per paper, site-wide
- 18 Dec 2019: We're pleased to announce PanLingua, a new tool that enables you to search for machine-translated bioRxiv preprints using more than 100 different languages.
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!