title: Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.
abstract: 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.
authors.affiliation: Department of Pharmacology, Vanderbilt University , Nashville, Tennessee 37232-6600, United States.|Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37240-7917, United States.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Bender
authors.affiliation: Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37240-7917, United States.|Chemical and Physical Biology Program, Vanderbilt University , Nashville, Tennessee 37232-0301, United States.
authors.forename: Alberto
authors.initials: A
authors.lastname: Cisneros
authors.affiliation: Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37240-7917, United States.|Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235, United States.
authors.forename: Amanda M
authors.initials: AM
authors.lastname: Duran
authors.affiliation: Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37240-7917, United States.|Department of Pathology, Microbiology and Immunology, Vanderbilt University , Nashville, Tennessee 37232-2561, United States.
authors.forename: Jessica A
authors.initials: JA
authors.lastname: Finn
authors.affiliation: Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37240-7917, United States.|Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235, United States.
authors.forename: Darwin
authors.initials: D
authors.lastname: Fu
authors.affiliation: Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37240-7917, United States.|Neuroscience Program, Vanderbilt University , Nashville, Tennessee 37235, United States.
authors.forename: Alyssa D
authors.initials: AD
authors.lastname: Lokits
authors.affiliation: Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37240-7917, United States.|Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235, United States.
authors.forename: Benjamin K
authors.initials: BK
authors.lastname: Mueller
authors.affiliation: Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37240-7917, United States.|Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235, United States.
authors.forename: Amandeep K
authors.initials: AK
authors.lastname: Sangha
authors.affiliation: Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37240-7917, United States.|Chemical and Physical Biology Program, Vanderbilt University , Nashville, Tennessee 37232-0301, United States.
authors.forename: Marion F
authors.initials: MF
authors.lastname: Sauer
authors.affiliation: Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37240-7917, United States.|Chemical and Physical Biology Program, Vanderbilt University , Nashville, Tennessee 37232-0301, United States.
authors.forename: Alexander M
authors.initials: AM
authors.lastname: Sevy
authors.affiliation: Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37240-7917, United States.|Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235, United States.
authors.forename: Gregory
authors.initials: G
authors.lastname: Sliwoski
authors.affiliation: Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37240-7917, United States.
authors.forename: Jonathan H
authors.initials: JH
authors.lastname: Sheehan
authors.affiliation: Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States.
authors.forename: Frank
authors.initials: F
authors.lastname: DiMaio
authors.affiliation: Department of Pharmacology, Vanderbilt University , Nashville, Tennessee 37232-6600, United States.|Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37240-7917, United States.|Chemical and Physical Biology Program, Vanderbilt University , Nashville, Tennessee 37232-0301, United States.|Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235, United States.|Department of Pathology, Microbiology and Immunology, Vanderbilt University , Nashville, Tennessee 37232-2561, United States.|Neuroscience Program, Vanderbilt University , Nashville, Tennessee 37235, United States.
authors.forename: Jens
authors.initials: J
authors.lastname: Meiler
authors.affiliation: Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37240-7917, United States.|Department of Chemistry, Vanderbilt University , Nashville, Tennessee 37235, United States.
authors.forename: Rocco
authors.initials: R
authors.lastname: Moretti
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D020407:Internet; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins; D012313:RNA