This chapter groups docking workflows that require peptide sequence input, two protein partners, or a PROTAC-linked ternary complex.
| Workflow | Starting material | Purpose |
|---|---|---|
| `peptide-docking{Peptide docking} | A prepared receptor and a table of peptide sequences | Sample peptide binding poses, including supported modifications and cyclization |
| `protprot{Protein-protein docking} | Structures of the two protein partners | Generate and refine candidate protein complexes |
| `protac{PROTAC modeling} | Target-ligand and ligase-ligand complexes plus the PROTAC structure | Model linker-compatible ternary complexes |
Peptide docking shares the receptor setup used for small molecules. Protein-protein and PROTAC workflows have their own setup and result interpretation, described in the corresponding sections below.