Applications for Macromolecule Design

General Protein Design

Fixed backbone design: Optimize sidechain-rotamer placement and identity on fixed backbones.
Fixed backbone design with hpatch: Fixed backone design with a penalty for hydrophobic survace patches.
Relax: When supplied with a resfile and the -relax:respect_resfile option, the relax application can be used for design.
Multistate design: Optimize proteins for multiple desired and undesired contexts.
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.
RosettaRemodel: Redesign backbone and sequence of protein loops and secondary structure elements.
- Remodel: Additional remodel documentation
Stepwise design: Simultaneously optimize sequence and structure for small RNA and protein segments. Part of the stepwise application.
SEWING: Build new protein structures from large elements (e.g. helix-loop-helix motifs) of native proteins.

Sequence tolerance: Optimize proteins for library applications (e.g. phage or yeast display).
SwiftLib server: Web-based tool for rapid optimization of degenerate codons.

Point mutation scan: Identifiy stabilizing point mutants.
Supercharge: Reengineer proteins for high net surface charges, to counter aggregation.
Void Identification and Packing (RosettaVIP): Identify and fill cavities in a protein.

Hydrogen bond surrogate design: Design stabilized alpha helical binders.
Beta strand homodimer design: Find proteins with surface exposed beta-strands, then design a homodimer that will form via that beta-strand.

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

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-ligand 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.