Job name
Molecules
Add one box per chain: Protein, Ligand, DNA, or RNA. Ligands take a SMILES string or a CCD_ code (e.g. CCD_ATP). A modification applies a CCD residue code at a given position; "Cyclic" marks the chain cyclic.
Protein chains
One protein chain sequence per line.
DNA chains (optional)
One DNA chain sequence per line.
RNA chains (optional)
One RNA chain sequence per line.
Molecules
JSON list of {"type": "protein"|"dna"|"rna", "chain": "A", "sequence": "..."}.
Design specification (YAML)
A complete Boltz YAML input, used as-is (ligands, bonds, restraints, templates below are ignored for this task).
Ligands (optional)
One ligand per line: a SMILES string, or CCD_<code> for a CCD component.
Predict affinity of the first ligand
Treat protein chains as cyclic
Use the public MSA server
Opt in to a network call to ColabFold's MMseqs2 server for better accuracy. Off by default keeps the run local (single-sequence mode).
Use inference-time potentials
Recycling steps
Diffusion sampling steps
Diffusion samples
Step scale (optional)
Diffusion temperature; lower increases diversity. Leave at 0 for Boltz's own default (~1.5).
Random seed
Output format
mmCIF
PDB
Covalent bonds (optional)
JSON list, e.g. [{"atom1Chain":"A","atom1Idx":32,"atom1Atom":"C","atom2Chain":"B","atom2Idx":1,"atom2Atom":"N"}].
Pocket restraints (optional)
JSON list, e.g. [{"binderChain":"A","pocketChain":"B","pocketContacts":"5 6 7","maxDistance":6,"force":false}].
Contact restraints (optional)
JSON list, e.g. [{"chainA":"A","res_idxA":1,"chainB":"B","res_idxB":1,"max_distance_angstrom":5,"force":false}].
Residue modifications (optional)
JSON list, e.g. [{"chain":"A","ptmPosition":15,"ptmResidue":"SEP"}].
Template structure (mmCIF, optional)
Uploaded mmCIF file used to template the prediction.
Template applies to chains (optional)
Comma-separated chain letters from above; blank matches automatically.
Template chain IDs (optional)
Comma-separated chain IDs inside the template mmCIF, aligned with the chains above.
Template distance threshold, angstrom (optional)