List of docking applications

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• Structure Prediction

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Options list

Antibody Docking

• Camelid antibody docking: Dock camelid antibodies to their antigens.
• SnugDock: Paratope structure optimization during antibody-antigen docking

NOTE: Use of command line apps is no longer recommended for ligand docking. Use RosettaScripts instead. See HighResDockerMover for example.

Ligand Docking

• Ligand docking (RosettaLigand): Determine the structure of protein-small molecule complexes.

  • Extract atomtree diffs: Extract structures from the AtomTreeDiff file format.

• Docking Approach using Ray-Casting (DARC): Docking method to specifically target protein interaction sites.

Peptide Docking

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

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.
    
  • Motif Dock Score: Efficient low-resolution protein-protein docking.

• Symmetric docking: Determine the structure of symmetric homooligomers.

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

See Also

• FunHunt, short for funnel hunt, tries to distinguish correct protein-protein complex orientations from decoy orientations.
• Application Documentation: List of Rosetta applications
• Rosetta Servers: Web-based interfaces to run some Rosetta applications
• Running Rosetta with options: Instructions for running Rosetta executables.
• RosettaScripts: Homepage for the RosettaScripts interface to Rosetta
• Comparing structures: Essay on comparing structures
• Analyzing Results: Tips for analyzing results generated using Rosetta
• Solving a Biological Problem: Guide to approaching biological problems using Rosetta
• Commands collection: A list of example command lines for running Rosetta executable files