Application Documentation

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.

Table of Contents

• Scripting interfaces to Rosetta functionality
• Structure Predition
• Docking
• Design
• Analysis
• Utilities
• Other

Scripting interfaces to Rosetta functionality

• RosettaScripts: An XML-based scripting interface
• PyRosetta: Python wrappings for Rosetta

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.

  • Membrane abinitio - Ab initio for membrane proteins.
    
  • Metalloprotein ab initio - Ab inito modeling of metalloproteins.
    

• Comparative modeling - Build structural models of proteins using one or more known structures as templates for modeling.

• RNA threading - Thread a new nucleotide sequence on an existing RNA structure.

• Fold-and-dock - Predict 3-dimentional structures of symetric homooligomers.

• Molecular replacement protocols - Use Rosetta to build models for use in X-ray crystrallography molecular replacement.

  • Prepare template for MR - Setup script for molecular replacement protocols.
    

• Relax - "Locally" optimize structures, including assigning sidechain positions.

• Backrub - Create backbone ensembles using small, local backbone changes.

• Floppy tail - Predict structures of long, flexible N-terminal or C-terminal regions.

Loop Modeling

• Loop modeling overview
• CCD loop modeling - Sample loop conformations using fragments and the CCD closure algorithm.
• Kinematic loop modeling - Sample loop conformations using the kinematic closure algorithm.
• Next-generation KIC - A newer version of loop modeling with kinematic closure.
• Stepwise assembly of protein loops - Generate three-dimensional de novo models of protein segments without surrounding sidechains.
  
  • Stepwise assembly of long loops - For loops greater than 4-5 residues.
    

RNA

• Rna denovo - Predict 3-dimensional structures of RNA from their nucleotide sequence.
• RNA loop modeling - Build RNA loops using deterministic stepwise assembly.
• RNA assembly with experimental constraints - Predict 3-dimensional structures of large RNAs with the help of experimental constraints
• ERRASER - Refine an RNA structure given electron density constraints.
  

Docking

Protein-Protein Docking

• Protein-Protein docking (RosettaDock) - Determine the structures of protein-protein complexes by using rigid body perturbations.

  • Docking prepack protocol - Prepare structures for protein-protein docking.
    

• Symmetric docking - Determine the structure of symmetric homooligomers.

• Chemically conjugated docking - Determine the structures of ubiquitin conjugated proteins.

Antibody Docking

• Antibody protocol (RosettaAntibody3) - Overview of the antibody modeling protocol.

  • Antibody Python script - The setup script.
    
  • 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.

• Camelid antibody docking - Dock camelid antibodies to their antigens.

Ligand Docking

• Ligand docking (RosettaLigand) - Determine the structure of protien-small molecule complexes.
  
  • Extract atomtree diffs - Extract structures from the AtomTreeDiff file format.
    

Peptide Docking

• Flexible peptide docking - Dock a flexible peptide to a protein.

Design

• Fixed backbone design - Optimize sidechain-rotamer placement and identity on fixed backbones.

  • Fixed backbone design with hpatch - Fixed backbone design with a penalty for hydrophobic surface patches.
    

• Void Indentification and Packing (RosettaVIP) - Identify and fill cavities in a protein.

• Point mutation scan - Identifiy stabilizing point mutants.

• Protein-protein design - Protein-protein interface design with RosettaScripts.

• Match - Place a small molecule into a protein pocket so it satisfies given geometric constraints.

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

• RosettaRemodel - Redesign backbone and sequence of protein loops and secondary structure elements.

  • Remodel - Additional remodel documentation

• Pepspec - Evaluate and design peptide-protein interactions.

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

• RNA design - Optimize RNA sequence for fixed backbones.

• Hydrogen bond surrogate design - Design stabilized alpha helical binders.

• OOP design - Design proteins with oligooxopiperazine residues.

• Multistate design - Optimize proteins for multiple desired and undesired contexts.

• Sequence tolerance - Optimize proteins for library applications (e.g. phage or yeast display).

• Anchored design - Design interfaces using an "anchor" of known interactions.

  • Anchored pdb creator - Prepare starting files for AnchoredDesign.
    
  • Anchor finder - Find interactions which can serve as "anchors" for AnchoredDesign.
    

• Supercharge - Reengineer proteins for high net surface charges, to counter aggregation.

• Zinc heterodimer design - Design zinc-mediated heterodimers.

• Beta strand homodimer design - Find proteins with surface exposed beta-strands, then design a homodimer that will form via that beta-strand.

• DougsDockDesignMinimize - Redesign the protein/peptide interface of Calpain and a fragment of its inhibitory peptide calpastatin.

Analysis

• Score - Calculate Rosetta energy for structures.

• Residue energy breakdown - Decompose scores into intra-residue and residue pair interactions.

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

• ddG monomer - Predict the change in stability (the ddG) of a monomeric protein induced by a point mutation.

• Interface analyzer - Calculate metrics evaluating interfaces.

Utilities

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

• Fragment picker - Pick fragments to be used in conjunction with other fragment-aware Rosetta applications.

  • Old fragment picker - The older version of the fragment picker.
    

• Cluster - Cluster structures by structural similarity.

• PyMol server - Observe what a running Rosetta program is doing by using PyMol.

• Build peptide - Build extended peptides or protein structures from sequences.

• CA to allatom - Build fullatom models from C-alpha-only traces.

• Create symmetry definition - Create Rosetta symmetry definition files for a point group.

  • Create symmetry definition from structure - Create Rosetta symmetry definition files from template PDBs.
    

• Non-canonical amino acids

  • Make rotamer library - Generate rotamer libraries for non-canonical amino acids.
    
  • Unfolded state energy calculator - Determine the baseline energy of non-canonical amino acids in the unfolded state.
    

• Loops from density - Create Rosetta loop files for regions of a protein with poor local fit to electron density.

• Sequence recovery - Calculate the mutations and native recovery from Rosetta design runs.

• OptE - Refit weights in a scorefunction to optimize given metrics.

Other

• Collection of example commandlines

• minirosetta - The "minirosetta" boinc wrapper application.