Rosetta is a suite of software libraries for macromolecular modeling. The diverse functionality of the libraries may be used by the end user in different ways:
- A set of premade applications define protocols that can be used to perform a specific task.
- A set of frameworks (PyRosetta, RosettaScripts) allow creation of your own protocols for new use cases.
- Various web servers, notably ROSIE, are set up and lend their computing power to provide applications that may be used remotely, without having to install anything on your computer.
A detailed list of protocols, frameworks and applications is available in the User Guide.
Use cases
Rosetta is best described by the science that our community, as well as other communities, have used it for. It is extendable and adaptable if you need it to be.
Protocols
Rosetta attempts to provide a flexible library of functionality to accomplish a diverse set of biomolecular modeling tasks. The basic tasks and operations that the libraries define, are combined together as algorithms which we call protocols, each of which use Rosetta’s flexible molecular modeling library to accomplish specific modeling tasks. These protocols can either be used as self contained units, or they can be chained together to accomplish more complex tasks, either by successive use of different applications or by combining the protocols within the generalizable frameworks. Rosetta algorithms are able to accomplish prediction, design and analysis on a diverse set of bio-molecular systems, including proteins, RNA, DNA, peptides, small molecules, and non-canonical or derivatized amino acids. Some protocols change/evaluate the internal structure of a single monomeric unit (loop remodeling, abinitio folding), while others model/evaluate the interaction between two seperate monomers (protein-protein docking, protein-peptide docking, protein-ligand docking). Many of these protocols can incorporate data from a variety of experimental results, including X-ray, NMR, and EPR. Rosetta protocols span a range of scales, from localized loop remodeling to full structure design, from single monomers to bio-molecular interactions to supra-molecular complexes.
Below is a partial list of protocols. For the full list, please advise the User Guide.
| RosettaAbinitio | De novo protein structure prediction. |
| RosettaDesign | Identifies low free energy sequences for target protein backbones. |
| Rosetta Design PyMol Plugin | PyMOL plugin A user-friendly interface for submitting Protein Design simulations using RosettaDesign. |
| RosettaDock | Predicts the structure of a protein-protein complex from the individual structures of the monomer components. |
| RosettaAntibody* | Predicts antibody Fv region structures. See PubMed 24519881 and 19062174. |
| RosettaFragments | Generates fragment libraries for use by Rosetta ab initio in building protein structures. |
| RosettaNMR | Incorporates NMR data into the basic Rosetta protocol to accelerate the process of NMR structure prediction |
| RosettaDNA | For the design of proteins that interact with specified DNA sequences. |
| RosettaRNA | Fragment assembly of RNA. |
| RosettaLigand | Small molecule – protein docking |
| RosettaSymmetry | Enforcing symmetry in Rosetta |
| RosettaEnzdes | Enzyme design |
| RosettaMembrane | Membrane protein ab initio modeling |
| RosettaDDG* | Estimating the impact of sequence changes on protein stability |
| RosettaScripts | An xml-based scripting language for control of modeling trajectories. Supports all major Rosetta functionalities |
| RosettaSnugDock* | Enables docking an antibody Fv region to an antigen and allows backbone flexibility in the paratope. |
| RosettaMultigraft | Performs matching, backbone, and side chain grafting of functional motifs onto scaffold proteins. |
| Rosetta FlexPepDock | Peptide-protein docking |
| Rosetta ERRASER | Remodeling RNA crystallographic models with electron density constraint. |
| RosettaVIP | Stabilize a protein by identifying and filling voids |
| RosettaMatdes | Materials design |
* marked applications might not be available in the latest version of Rosetta