Protocols for Molecular Modeling with Rosetta3 and RosettaScripts

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.