期刊
BIOCHEMISTRY
卷 55, 期 34, 页码 4748-4763出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.biochem.6b00444
关键词
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资金
- National Institutes of Health (NIH) [R01GM073151]
- RosettaCommons
- NIH [R01 GM080403, R01 GM099842, R01 DK097376, R01 HL122010, R01 GM073151, U19 AI117905]
- National Science Foundation [CHE 1305874]
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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