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.


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.

Carbohydrate Modeling

Apps

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

  • 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.
  • 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.

Docking

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


Design

General

Stability Improvement

Enzymes

  • Enzyme Design - Design a protein around a small molecule, with catalytic constraints.

Peptides

  • Pepspec - Evaluate and design peptide-protein interactions.

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

  • 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.

DNA

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

Secondary Structure


Membrane Proteins

Getting Started

Key Elements in RosettaMP

Applications

  • 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.

Analysis

Scoring

  • 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.

  • cartesian-ddg - A different version of ddg calculation, using Cartesian space sampling

  • Density map scoring - Score structures with electron density information.

Clustering

  • calibur - (Preferred application) Cluster structures using a port of calibur into Rosetta .

  • cluster - Original Rosetta++ app. Fails at large number of decoys

Constraints

  • 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

Interfaces

Peptides

  • 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

Utilities

These applications serve mainly to support other Rosetta applications, or to assist in setting up or analyzing Rosetta runs.

General

Non-canonical amino acids

Other

See Also