{
"fields": [
{
"name": "job_name",
"label": "Job name",
"kind": "text",
"default": "boltz2-demo",
"required": false,
"help": "Names the output directory for this run.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": 80,
"accept": "",
"task": "",
"group": "Input"
},
{
"name": "sequence_molecules",
"label": "Molecules",
"kind": "molecule_builder",
"default": "[{\"type\": \"protein\", \"id\": \"A\", \"sequence\": \"QLEDSEVEAVAKGLEEMYANGVTEDNFKNYVKNNFAQQEIS\", \"msa\": \"empty\", \"cyclic\": false, \"modifications\": []}]",
"required": true,
"help": "Add one box per unique protein, ligand, DNA, or RNA entity. Set its native Boltz chain ID (or comma-separated IDs for identical copies), sequence or ligand, optional protein MSA, cyclic flag, and residue modifications.",
"options": [
{
"value": "protein",
"label": "Protein"
},
{
"value": "ligand",
"label": "Ligand"
},
{
"value": "dna",
"label": "DNA"
},
{
"value": "rna",
"label": "RNA"
}
],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Input",
"input_modes": "parameters",
"molecule_features": "id,cyclic,modifications,protein_msa"
},
{
"name": "constraints",
"label": "Constraints (JSON, optional)",
"kind": "textarea",
"default": "",
"required": false,
"help": "Native Boltz constraints array. Supports bond, pocket, and contact entries using the chain IDs above.",
"options": [],
"rows": 6,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": 500000,
"accept": "",
"task": "",
"group": "Input",
"input_modes": "parameters"
},
{
"name": "templates",
"label": "Templates (JSON, optional)",
"kind": "textarea",
"default": "",
"required": false,
"help": "Native Boltz templates array. Each entry may select a CIF/PDB, chain mapping, force flag, and threshold.",
"options": [],
"rows": 6,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": 500000,
"accept": "",
"task": "",
"group": "Input",
"input_modes": "parameters"
},
{
"name": "properties",
"label": "Properties (JSON, optional)",
"kind": "textarea",
"default": "",
"required": false,
"help": "Native Boltz properties array, such as [{\"affinity\": {\"binder\": \"B\"}}].",
"options": [],
"rows": 4,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": 500000,
"accept": "",
"task": "",
"group": "Input",
"input_modes": "parameters"
},
{
"name": "yaml_spec",
"label": "Boltz input (YAML)",
"kind": "textarea",
"default": "version: 1\nsequences:\n - protein:\n id: A\n sequence: QLEDSEVEAVAKGLEEMYANGVTEDNFKNYVKNNFAQQEIS\n msa: empty\n",
"required": true,
"help": "Complete native Boltz YAML. Define protein, DNA, RNA, and ligand entities under sequences; optional constraints, templates, and affinity properties use the same schema as the Boltz CLI.",
"options": [],
"rows": 16,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": 500000,
"accept": "",
"task": "",
"group": "Input",
"help_note": "Bio Web writes this text to input.yaml and passes that file to boltz predict.",
"input_modes": "text"
},
{
"name": "inputs_file",
"label": "Boltz input file (YAML)",
"kind": "file",
"default": "",
"required": false,
"help": "The YAML file defining this prediction, in the same schema as the Boltz CLI takes.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": ".yaml,.yml,.json",
"task": "",
"group": "Input",
"input_modes": "upload",
"help_note": "Choose a file. Its contents are read here and sent as the input document."
},
{
"name": "use_msa_server",
"label": "Use the public MSA server",
"kind": "checkbox",
"default": false,
"required": false,
"help": "Generate missing protein MSAs through Boltz's configured MMseqs2 server. Leave off when every protein supplies an MSA path or uses msa: empty.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Inference"
},
{
"name": "use_potentials",
"label": "Use inference-time potentials",
"kind": "checkbox",
"default": false,
"required": false,
"help": "Apply Boltz-2 inference-time potentials to improve physical plausibility.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Inference"
},
{
"name": "recycling_steps",
"label": "Recycling steps",
"kind": "number",
"default": 3,
"required": false,
"help": "Number of recycling steps. The Boltz CLI default is 3.",
"options": [],
"rows": null,
"minimum": 1,
"maximum": 20,
"step": 1,
"maxlength": null,
"accept": "",
"task": "",
"group": "Inference"
},
{
"name": "sampling_steps",
"label": "Structure sampling steps",
"kind": "number",
"default": 200,
"required": false,
"help": "Diffusion steps used for structure prediction. The Boltz CLI default is 200.",
"options": [],
"rows": null,
"minimum": 10,
"maximum": 1000,
"step": 1,
"maxlength": null,
"accept": "",
"task": "",
"group": "Inference"
},
{
"name": "diffusion_samples",
"label": "Structure samples",
"kind": "number",
"default": 1,
"required": false,
"help": "Independent diffusion samples generated for each input.",
"options": [],
"rows": null,
"minimum": 1,
"maximum": 50,
"step": 1,
"maxlength": null,
"accept": "",
"task": "",
"group": "Inference"
},
{
"name": "step_scale",
"label": "Structure step scale",
"kind": "number",
"default": 1.5,
"required": false,
"help": "Diffusion temperature/step size. Boltz-2 defaults to 1.5 and recommends values between 1 and 2; lower values increase diversity.",
"options": [],
"rows": null,
"minimum": 0,
"maximum": 5,
"step": 0.01,
"maxlength": null,
"accept": "",
"task": "",
"group": "Inference"
},
{
"name": "sampling_steps_affinity",
"label": "Affinity sampling steps",
"kind": "number",
"default": 200,
"required": false,
"help": "Sampling steps for the affinity head. Used only when the YAML requests an affinity property.",
"options": [],
"rows": null,
"minimum": 1,
"maximum": 1000,
"step": 1,
"maxlength": null,
"accept": "",
"task": "",
"group": "Affinity"
},
{
"name": "diffusion_samples_affinity",
"label": "Affinity samples",
"kind": "number",
"default": 5,
"required": false,
"help": "Diffusion samples for the affinity head. The Boltz CLI default is 5.",
"options": [],
"rows": null,
"minimum": 1,
"maximum": 50,
"step": 1,
"maxlength": null,
"accept": "",
"task": "",
"group": "Affinity"
},
{
"name": "affinity_mw_correction",
"label": "Apply affinity molecular-weight correction",
"kind": "checkbox",
"default": false,
"required": false,
"help": "Enable Boltz's molecular-weight correction for the affinity value head.",
"options": [],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Affinity"
},
{
"name": "seed",
"label": "Random seed",
"kind": "number",
"default": 0,
"required": false,
"help": "Seed used by the Boltz random-number generator.",
"options": [],
"rows": null,
"minimum": 0,
"maximum": 4294967295,
"step": 1,
"maxlength": null,
"accept": "",
"task": "",
"group": "Output"
},
{
"name": "output_format",
"label": "Coordinate format",
"kind": "select",
"default": "mmcif",
"required": false,
"help": "Format of predicted coordinate files.",
"options": [
{
"value": "mmcif",
"label": "mmCIF"
},
{
"value": "pdb",
"label": "PDB"
}
],
"rows": null,
"minimum": null,
"maximum": null,
"step": null,
"maxlength": null,
"accept": "",
"task": "",
"group": "Output"
}
],
"input_modes": {
"name": "input_mode",
"label": "Input mode",
"default": "parameters",
"options": [
{
"value": "parameters",
"label": "Set parameters here"
},
{
"value": "text",
"label": "Enter YAML or JSON"
},
{
"value": "upload",
"label": "Upload YAML or JSON"
}
]
},
"tasks": []
}