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Protocols for Molecular Modeling with Rosetta3 and RosettaScripts

Version 3 2016-08-24, 17:15
Version 2 2016-08-17, 12:57
Version 1 2016-08-16, 14:18
Posted on 2016-08-04 - 00:00
Previously, we published an article providing an overview of the Rosetta suite of biomacromolecular modeling software and a series of step-by-step tutorials [Kaufmann, K. W., et al. (2010) Biochemistry 49, 2987–2998]. The overwhelming positive response to this publication we received motivates us to here share the next iteration of these tutorials that feature de novo folding, comparative modeling, loop construction, protein docking, small molecule docking, and protein design. This updated and expanded set of tutorials is needed, as since 2010 Rosetta has been fully redesigned into an object-oriented protein modeling program Rosetta3. Notable improvements include a substantially improved energy function, an XML-like language termed “RosettaScripts” for flexibly specifying modeling task, new analysis tools, the addition of the TopologyBroker to control conformational sampling, and support for multiple templates in comparative modeling. Rosetta’s ability to model systems with symmetric proteins, membrane proteins, noncanonical amino acids, and RNA has also been greatly expanded and improved.

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Biochemistry

AUTHORS (15)

  • Brian J. Bender
    Alberto Cisneros
    Amanda M. Duran
    Jessica A. Finn
    Darwin Fu
    Alyssa D. Lokits
    Benjamin K. Mueller
    Amandeep K. Sangha
    Marion F. Sauer
    Alexander M. Sevy
    Gregory Sliwoski
    Jonathan H. Sheehan
    Frank DiMaio
    Jens Meiler
    Rocco Moretti
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