Below is a list of the currently released applications containing developer documentation. Click on an application to see a more detailed description of the purpose and for detailed examples. If a released application is missing, please file a bug in our issue tracker.
If you are unsure which application best fits your biological problem, you may want to start here.
A collection of example command lines can be found here.
Table of Contents
While most of these applications focus on prediction, many have options which will also allow design.
Comparative modeling - Build structural models of proteins using one or more known structures as templates for modeling.
Floppy tail - Predict structures of long, flexible N-terminal or C-terminal regions.
| Application | Description |
|---|---|
| GlycanRelax | Model glycan trees using known carbohydrate information. Works for full denovo modeling or refinement. |
| GlycanInfo | Get information on all glycan trees within a pose |
| GlycanClashCheck | Obtain data on model clashes with and between glycans, or between glycans and other protein chains. |
| Component | Description |
|---|---|
| GlycanRelaxMover | Model glycan trees using known carbohydrate information. Works for full denovo modeling or refinement. |
| SimpleGlycosylateMover | Glycosylate poses with glycan trees. |
| GlycanTreeSelector | Select individual glcyan trees or all of them |
| GlycanResidueSelector | Select specific residues of each glycan tree of interest. |
Ligand docking (RosettaLigand) - Determine the structure of protein-small molecule complexes.
Docking Approach using Ray-Casting (DARC) - Docking method to specifically target protein interaction sites.
Terpene docking - Terdockin: Docking protocol for terpene synthases.
Protein-Protein docking (RosettaDock) - Determine the structures of protein-protein complexes by using rigid body perturbations.
Symmetric docking - Determine the structure of symmetric homooligomers.
Chemically conjugated docking - Determine the structures of ubiquitin conjugated proteins.
Fixed backbone design - Optimize sidechain-rotamer placement and identity on fixed backbones.
Multistate design - Optimize proteins for multiple desired and undesired contexts.
Anchored design - Design interfaces using an "anchor" of known interactions.
Create clash-based repack shell -- Supplement a design resfile with residues which may clash.
RosettaAntibodyDesign - Design Antibodies and Antibody-Antigen complexes
RECON multistate design - Multi-specificity design to optimize proteins for recognition of multiple targets.
revert-design-to-native - Get energetic contribution of designed residues to predicted binding energy
RosettaRemodel - Redesign backbone and sequence of protein loops and secondary structure elements.
curvedsheetdesign - Design backbones for curved beta sheets
Sequence tolerance - Optimize proteins for library applications (e.g. phage or yeast display).
Stepwise design - Simultaneously optimize sequence and structure for small RNA and protein segments. Part of the stepwise application.
Zinc heterodimer design - Design zinc-mediated heterodimers.
Biased forward folding - Select de novo designed proteins for ab initio structure prediction.
Point mutation scan - Identifiy stabilizing point mutants.
Supercharge - Reengineer proteins for high net surface charges, to counter aggregation.
Void Identification and Packing (RosettaVIP) - Identify and fill cavities in a protein.
Enzyme Design - Design a protein around a small molecule, with catalytic constraints.
RosettaEnzCM - Calculates the average atomic distances from template catalytic residues to be used for distance constraints for RosettaCM.
Match - Place a small molecule into a protein pocket so it satisfies given geometric constraints.
OOP design - Design proteins with oligooxopiperazine residues.
DougsDockDesignMinimize - Redesign the protein/peptide interface of Calpain and a fragment of its inhibitory peptide calpastatin.
theta ligand - Calculate the fraction of ligand that is exposed to the solvent in a protein-ligan complex.
RNA design - Optimize RNA sequence for fixed backbones.
Stepwise design - Simultaneously optimize sequence and structure for small RNA and protein segments. Part of the stepwise application.
Hydrogen bond surrogate design - Design stabilized alpha helical binders.
Beta strand homodimer design - Find proteins with surface exposed beta-strands, then design a homodimer that will form via that beta-strand.
Score - Calculate Rosetta energy for structures.
Residue energy breakdown - Decompose scores into intra-residue and residue pair interactions.
ddG monomer - Predict the change in stability (the ddG) of a monomeric protein induced by a point mutation.
flex ddG - Predict change in interaction energy at a protein-protein interface post-mutation. Benchmarked to work for single point mutations or sets of multiple mutations. Slower than some other protocols since more sampling is included, but is particularly useful for multiple mutations or small-to-large mutations in interfaces.
cartesian-ddg - A different version of ddg calculation, using Cartesian space sampling
Density map scoring - Score structures with electron density information.
calibur - (Preferred application) Cluster structures using a port of calibur into Rosetta .
cluster - Original Rosetta++ app. Fails (i.e silently produces meaningless results) at large number of decoys.
energy_based_clustering - A fast energy-based clustering approach optimized for large numbers of structures.
Workbench - UI front end to submit Rosetta jobs from desktop client
These applications serve mainly to support other Rosetta applications, or to assist in setting up or analyzing Rosetta runs.
Build peptide - Build extended peptides or protein structures from sequences.
Dump a capped residue - Output a PDB file containing a residue (specifiable by name), with options that can control polymeric patch state
CA to allatom - Build fullatom models from C-alpha-only traces.
Create symmetry definition - Create Rosetta symmetry definition files for a point group.
Batch distances - Calculate the closest approach for residue-residue pairs.
Fragment picker - Pick fragments to be used in conjunction with other fragment-aware Rosetta applications.
Make exemplars - Create an exemplar for surface pockets on a protein that touch a target residue.
OptE - Refit reference weights in a scorefunction to optimize given metrics.
Pocket target residue suggestion - Suggest the best pair of target residues for pocket optimization for the purpose of inhibiting a protein-protein interaction.
Pocket relax - Relax followed by full atom minimization and scoring with no PocketConstraint. Useful when performing pocket optimization.
PyMol server - Observe what a running Rosetta program is doing by using PyMol.
Residue Type Converter - Convert Rosetta residue type specification formats between each other.
Sequence recovery - Calculate the mutations and native recovery from Rosetta design runs.
Torsional potential correction - Remove double counting interactions from the sidechain torsional potential
| Application | Description |
|---|---|
| DNA_methylation | Simulate the action of a virtual DNA methyltransferase enzyme on a .pdb file. |
| glycosyltransfer | Simulate the action of a virtual glycosyltransferase (GT) or oligosacharyltransferase (OST) enzyme on a .pdb file. |
| phosphorylation | Simulate the action of a virtual kinase enzyme on a .pdb file. |
| N-terminal_acetyltransfer | Simulate the action of a virtual N-terminal acetyltransferase (NAT) enzyme on a .pdb file. |
minirosetta - The "minirosetta" boinc wrapper application.
Tools: List of useful accessory scripts included with Rosetta