boltz2.yaml

# Boltz-2 Model Configuration
# Structure prediction via diffusion

id: boltz2
name: Boltz-2
version: "2.9.5"
category: structure_prediction
description: >
  Diffusion-based structure prediction from sequences. Predicts protein
  structure, confidence scores, and can handle protein-ligand complexes.
  Primary structure validator for BioModStack designs.
container: boltz2.sif

ui_icon: cube
ui_color: "#3B82F6"

inputs:
  - fasta
  - yaml
outputs:
  - pdb
  - json

modes:
  - id: predict
    name: Structure Prediction
    description: Predict structure from sequence
    params:
      - colabfold_use_env
      - colabfold_use_filter
      - colabfold_use_templates
      - colabfold_pairing_mode
      - colabfold_pairing_strategy
      - msa_provider
      - msa_neurosnap_coverage_percent
      - msa_neurosnap_identity_percent
      - msa_neurosnap_max_sequences
      - msa_neurosnap_force_uppercase
      - msa_neurosnap_pad_sequences
      - sequence
      - sequence_name
      - boltz_recycling_steps
      - boltz_diffusion_samples
      - boltz_max_parallel_samples
      - boltz_sampling_steps
      - boltz_use_msa
      - boltz_method
      - num_parallel_jobs

  - id: complex
    name: Complex Prediction
    description: Predict protein-ligand or protein-protein complex
    params:
      - colabfold_use_env
      - colabfold_use_filter
      - colabfold_use_templates
      - colabfold_pairing_mode
      - colabfold_pairing_strategy
      - msa_provider
      - msa_neurosnap_coverage_percent
      - msa_neurosnap_identity_percent
      - msa_neurosnap_max_sequences
      - msa_neurosnap_force_uppercase
      - msa_neurosnap_pad_sequences
      - sequence
      - sequence_name
      - boltz_recycling_steps
      - boltz_diffusion_samples
      - boltz_max_parallel_samples
      - boltz_sampling_steps
      - boltz_use_potentials
      - boltz_use_msa
      - boltz_method
      - num_parallel_jobs

params:
  - name: colabfold_use_env
    type: boolean
    description: "ColabFold API only — Include environmental sequence databases. Native use_env."
    default: true

  - name: colabfold_use_filter
    type: boolean
    description: "ColabFold API only — Filter alignments; unfiltered paired search unsupported. Native use_filter."
    default: true

  - name: colabfold_use_templates
    type: boolean
    description: "ColabFold API only — Retrieve templates; unsupported by the current MSA artifact contract. Native use_templates."
    default: false

  - name: colabfold_pairing_mode
    type: string
    description: "ColabFold API only — Unpaired, paired, or both alignment roles; paired requires distinct chains. Native pairing_mode."
    default: unpaired
    enum: ["unpaired", "paired", "unpaired_paired"]

  - name: colabfold_pairing_strategy
    type: string
    description: "ColabFold API only — ColabFold species pairing strategy. Native pairing_strategy."
    default: greedy
    enum: ["greedy", "complete"]

  - name: msa_provider
    type: string
    description: "External MSA provider; auto selects ColabFold. Local disabled. Unsupported consumer/output combinations fail admission."
    default: colabfold_api
    enum: [auto, colabfold_api, neurosnap_api]

  - name: msa_neurosnap_coverage_percent
    type: number
    description: "Neurosnap API only — Coverage: Minimum query coverage (%)."
    default: 35
    minimum: 10
    maximum: 90

  - name: msa_neurosnap_identity_percent
    type: number
    description: "Neurosnap API only — Identity threshold: Provider minimum identity to query (%); not local redundancy filtering."
    default: 50
    minimum: 25
    maximum: 100

  - name: msa_neurosnap_max_sequences
    type: integer
    description: "Neurosnap API only — Max Sequences: Final MSA depth limit."
    default: 1000000
    minimum: 10
    maximum: 1000000

  - name: msa_neurosnap_force_uppercase
    type: boolean
    description: "Neurosnap API only — Force Uppercase: Uppercase residues including A3M insertions; consumer compatibility required."
    default: false

  - name: msa_neurosnap_pad_sequences
    type: boolean
    description: "Neurosnap API only — Pad Sequences: C-terminal gap padding to longest row; consumer compatibility required."
    default: false

  # Input sequence
  - name: sequence
    type: text
    description: Amino acid sequence to predict
    required: true
    preset_type: sequence

  - name: sequence_name
    type: string
    description: Name for output structure files
    required: false
    default: predicted

  - name: boltz_recycling_steps
    type: integer
    description: Number of recycling iterations
    required: false
    default: 3
    minimum: 1
    maximum: 10

  - name: boltz_diffusion_samples
    type: integer
    description: Number of final ranked candidate structures to generate from the same input
    required: false
    default: 1
    minimum: 1
    maximum: 32

  - name: boltz_max_parallel_samples
    type: integer
    description: Denoiser-forward chunk limit for already-requested Boltz diffusion samples; lower can reduce neural-network VRAM spikes but is not full job-level serialization
    required: false
    default: 1
    minimum: 1
    maximum: 32

  - name: boltz_sampling_steps
    type: integer
    description: Number of diffusion sampling steps (higher = better quality)
    required: false
    default: 200
    minimum: 1
    maximum: 1000

  - name: num_parallel_jobs
    type: integer
    description: Number of parallel simulation jobs to run
    required: false
    default: 1
    minimum: 1
    maximum: 500


  - name: boltz_use_potentials
    type: boolean
    description: Use physics-based potentials (Boltz-2x mode) for better accuracy
    required: false
    default: false

  - name: boltz_use_msa
    type: boolean
    description: Use MSA features with the selected external provider or verified supplied alignments; local search disabled
    required: false
    default: true

  - name: boltz_method
    type: string
    description: Experimental Method Conditioning
    required: false
    default: ""
    enum:
      - ""
      - md
      - x-ray diffraction
      - electron microscopy
      - solution nmr
      - solid-state nmr
      - neutron diffraction
      - electron crystallography
      - fiber diffraction
      - powder diffraction
      - infrared spectroscopy
      - fluorescence transfer
      - epr
      - theoretical model
      - solution scattering
      - other
      - afdb
      - boltz-1

  - name: boltz_extra_config
    type: string
    description: "Additional Boltz-2 parameters (e.g., '--msa_pairing_strategy complete')"
    required: false

enabled: true
experimental: false