Preprint Article Version 2 This version is not peer-reviewed

Macromolecular Modeling and Design in Rosetta: New Methods and Frameworks

Version 1 : Received: 21 April 2019 / Approved: 24 April 2019 / Online: 24 April 2019 (10:16:38 CEST)
Version 2 : Received: 29 April 2019 / Approved: 8 May 2019 / Online: 8 May 2019 (08:24:25 CEST)

How to cite: Koehler Leman, J.; Weitzner, B.D.; Lewis, S.M.; Consortium, R.; Bonneau, R. Macromolecular Modeling and Design in Rosetta: New Methods and Frameworks. Preprints 2019, 2019040263 Koehler Leman, J.; Weitzner, B.D.; Lewis, S.M.; Consortium, R.; Bonneau, R. Macromolecular Modeling and Design in Rosetta: New Methods and Frameworks. Preprints 2019, 2019040263

Abstract

The Rosetta software suite for macromolecular modeling, docking, and design is widely used in pharmaceutical, industrial, academic, non-profit, and government laboratories. Considering its broad modeling capabilities, Rosetta consistently ranks highly when compared to other leading methods created for highly specialized protein modeling and design tasks. Developed for over two decades by a global community of scientists at more than 60 institutions, Rosetta has undergone multiple refactorings, and now comprises over three million lines of code. Here we discuss the methods developed in the last five years, involving the latest protocols for structure prediction, protein–protein and protein–small molecule docking, protein structure and interface design, loop modeling, the incorporation of various types of experimental data, and modeling of peptides, antibodies and other proteins in the immune system, nucleic acids, non-standard amino acids, carbohydrates, and membrane proteins. We briefly discuss improvements to the energy function, user interfaces, and usability of the ­­software. Rosetta is available at www.rosettacommons.org.

Subject Areas

structure prediction; Rosetta; computational modeling; protein design

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