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

Scripting interfaces to Rosetta functionality

Structure Prediction

While most of these applications focus on prediction, many have options which will also allow design.

  • Ab initio modeling - Predict 3-dimensional structures of proteins from their amino acid sequences.
  • Backrub - Create backbone ensembles using small, local backbone changes.
  • 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.

  • Fold-and-dock - Predict 3-dimensional structures of symmetric homooligomers.
  • Helical bundle structure prediction - Predict structures of predominantly helical heteropolymers from sequence. Uses a fragment-free approach that is good for proteins and non-natural heterpolymers with no close relatives of known structure. Experimental.
  • Molecular replacement protocols - Use Rosetta to build models for use in X-ray crystrallography molecular replacement.
  • Relax - "Locally" optimize structures, including assigning sidechain positions.
  • RNA - see below for apps, including FARFAR & ERRASER (crystallographic refinement).
  • Simple Cyclic Peptide Prediction - Prediction of structures of small (~5-20 residue) backbone-cyclized peptides consisting of any mixture of L- and D-amino acids.
  • trRosetta application - Predict structures of canonical single-chain proteins without fragments, using the trRosetta neural network and gradient-descent minimization.
  • RosettaNMR with Paramagnetic Restraints - Structure prediction in RosettaNMR using backbone chemical shifts and paramagnetic restraints derived from metal ion tags.

Antibody Modeling

  • Antibody protocol (RosettaAntibody3) - Overview of the antibody modeling protocol.
    • Grafting CDR loops - Graft antibody CDR templates on the framework template to create a rough antibody model.
    • Modeling CDR H3 - Determine antibody structures by combining VL-VH docking and H3 loop modeling.

T Cell Receptor Modeling

Carbohydrate Modeling


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.

RosettaScript Components

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.

Loop Modeling

RNA and RNA/protein

  • FARFAR2 - Predict whole RNA structures in one step
  • RNA structure prediction - Predict 3-dimensional structures of RNA from their nucleotide sequence. Read this first.
    • RNA tools - Tools useful for RNA and RNA/proteinm including general PDB editing, cluster submission, job setup.
    • RNA threading - Thread a new nucleotide sequence on an existing RNA structure.
    • RNA motif prediction - Model RNA motifs with fragment assembly of RNA with full atom refinement (FARFAR).
    • CS Rosetta RNA: Refines and scores an RNA structure using NMR chemical shift data.
  • RNA stepwise loop enumeration - Build RNA loops using deterministic stepwise assembly. See also Stepwise monte carlo.
  • Stepwise monte carlo - Generate 3D models of protein, RNA, and protein/RNA loops, motifs, and interfaces. Stochastic version of stepwise assembly.
  • RNA assembly with experimental constraints - Predict 3-dimensional structures of large RNAs with the help of experimental constraints. Note – largely deprecated by newer pipeline (documentation coming soon).
  • ERRASER - Refine an RNA structure given electron density constraints.
  • ERRASER2 - An update to ERRASER that eliminates the need for a particular Python environment and Phenix evaluation, in favor of exclusively internal Rosetta tools. Still unpublished/officially "beta."
  • DRRAFTER - Build RNA coordinates into cryoEM maps of RNA-protein assemblies.
  • auto-DRRAFTER - Automatically build RNA coordinates into cryo-EM maps (currently for maps that do not contain proteins).
  • Sample around nucleobase - Visualizing energy functions by scanning probe molecules around a nucleobase.
  • RECCES - RNA free energy calculation with comprehensive sampling.
  • RNA pharmacophore - Extract and cluster the key features present in RNA (rings, hbond donors & acceptors) from the structure of a protein-RNA complex.


Antibody Docking

Ligand Docking

Peptide Docking

Protein-Protein Docking

Ion docking

  • Mg(2+) modeling - Basic code for docking Mg(2+) -- with or without explicit waters -- initially tested for RNA.

Protein-Surface Docking



Stability Improvement


  • 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.


  • Pepspec - Evaluate and design peptide-protein interactions.
  • Count Cycpep Sequences - Counts the number of unique sequences possible for a macrocycle given P possible building blocks and n residues, with options for CN and SN symmetry. Evaluates the number using analytic expressions derived from Burnside's lemma, and optionally compares to counts performed by brute-force enumeration.

Small Molecules

  • 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.


  • Rosetta DNA (RosettaDNA) - Design and model protein interactions to DNA.

Secondary Structure

Membrane Proteins

Getting Started

Key Elements in RosettaMP


  • Relax:
    • mp_relax - High-resolution refinement of membrane protein structures with optimization of the membrane position using minimization (uses membrane framework and FastRelax)
  • ddG:
    • mp_ddG - Prediction of free energy changes upon mutation using the membrane framework
  • Docking:
    • mp_dock - Protein-protein docking in the membrane (uses membrane framework)
    • mp_dock_setup - Setup tools required to run MPDock
    • mp_symdock - Assemble symmetric complexes in the membrane environment (uses membrane framework)
  • Viewer:
    • mp_viewer - Standalone application for visualization of membrane protein simulations in real-time using pymol (uses membrane framework)
  • Tools:
    • score_jd2 - Settings for using score_jd2 with the RosettaMP scoring functions.
    • mp_span_from_pdb - Calculate trans-membrane spans from the PDB structure
    • mp_transform - Transforming the protein into membrane coordinates.
  • Structure prediction:
  • Homology modeling:
    • RosettaCM membrane - Multi-template homology modeling based on RosettaCM and RosettaMembrane
  • Lipid accessibility:
    • mp_lipid_acc - Compute per-residue lipid accessibility from structure
  • Domain assembly:
    • mp_domain_assembly - Create full-length model of a membrane protein from known domain structures




  • 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.


  • Constraint Info - Get information about how a structure matches Rosetta constraints.

Feature Reporter Framework

  • FeatureReporters - Framework for the analysis, and comparison of various features of PDB structures
  • FeaturesTutorials - Tutorials for the Feature Reporter Analysis Framework



  • PeptiDerive - derives from a given interface the linear stretch that contributes most of the binding energy.

Packing Quality

  • RosettaHoles - Rapid assessment of protein core packing for structure prediction, design, and validation

Surface pockets

Buried unsatisfied polar atoms

  • shobuns - Identifies polar atoms that are buried unsatisfied for the SHO model of polar solvation

Residue disorder prediction

Residue Solvent Exposure

Surface-induced dissociation (SID) energy-resolved mass spectrometry (ERMS) data prediction


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.

Non-canonical amino acids

Post-Translational Modifications


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.

Mover Components

  • EnzymaticMover - Documentation about the underlying code used for post-translational modifications in Rosetta.


See Also