Job name
Structure
Chains to design (optional)
Comma-separated chain IDs; blank designs every chain in the structure.
Batch size
Sequences generated = batch_size x number_of_batches.
Number of batches
Sampling temperature
Random seed
Omit amino acids (optional)
One-letter amino-acid codes to never sample, e.g. "CX".
Amino-acid bias (optional)
Global per-amino-acid sampling bias, e.g. "A:-1.0,P:2.3".
Per-residue amino-acid bias (optional)
JSON object keyed by chain+residue, e.g. {"C1": {"G": -0.3, "P": 10.8}}.
Per-residue omitted amino acids (optional)
JSON object keyed by chain+residue, e.g. {"A1": "ACDEFG"}.
Fixed residues (optional)
Space-separated "ChainResnum", e.g. "C1 C2 C3"; these residues are held fixed.
Redesigned residues (optional)
Space-separated "ChainResnum", the inverse of fixed_residues: only these are redesigned.
Tie designed chains as a homo-oligomer
Symmetric copies: ties equivalent positions across all designed chains to the same amino acid.
Use nearby ligand atoms as context
Use fixed residues' side chains as ligand context
Ligand context cutoff, angstrom
Buried transmembrane residues
Space-separated "ChainResnum", e.g. "A1 A2 A3".
Interface-facing transmembrane residues
Space-separated "ChainResnum".
Transmembrane protein
No
Yes
Pack side chains onto designed backbones
Side-chain packs per design
0 uses a single fast pack instead of resampling.
Pack side chains with ligand context
Repack fixed residues' side chains too
Off keeps fixed residues' side chains exactly as given.