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.
CA to allatom: Build fullatom models from C-alpha-only traces.
Cluster: Cluster structures by structural similarity.
Create symmetry definition: Create Rosetta symmetry definition files for a point group.
Fragment picker: Pick fragments to be used in conjunction with other fragment-aware Rosetta applications.
Loops from density: Create Rosetta loop files for regions of a protein with poor local fit to electron density.
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.
PyMol server: Observe what a running Rosetta program is doing by using PyMol.
Sequence recovery: Calculate the mutations and native recovery from Rosetta design runs.
Pocket relax: Relax followed by full atom minimization and scoring with no PocketConstraint. Useful when performing pocket optimization.
Antibody Design Strategy Analysis: A PyRosetta-based tool to analyze and/or compare antibody design strategies.
CDR Cluster Identification: An application that matches each CDR of an antibody to North/Dunbrack CDR clusters based on the lowest dihedral distance to each cluster center.
CDR Cluster Constrained Relax: An application to relax CDRs using circular harmonic constraints based on identified CDR clusters.