BioModStack/platform/api/config/models/docking.yaml at main · MolBioFreak/BioModStack · GitHub

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# Dual Docking - Parallel DiffDock + Uni-Dock with Comparison
#
# Runs both ML-based (DiffDock) and physics-based (Uni-Dock) docking in parallel.
# Provides orthogonal validation through pose comparison and consensus scoring.

id: docking
name: Dual Docking
version: "1.0.0"
category: docking
description: >
  Run both DiffDock (ML) and Uni-Dock (physics) in parallel for orthogonal validation.
  Compare poses via RMSD and get consensus scoring for higher-confidence predictions.
container: diffdock.sif

ui_icon: equals
ui_color: "#8B5CF6"

inputs:
  - pdb
  - smiles
outputs:
  - pdb
  - json

modes:
  - id: compare
    name: Compare Methods
    description: >
      Run both docking engines, compare poses side-by-side.
      See RMSD between top poses and identify agreements/disagreements.
    params:
      - protein_pdb
      - ligand_smiles
      - ntp_type
      - num_poses
      - exhaustiveness
      - scoring_function
      - box_size
      - inference_steps
      - affinity_threshold
      - confidence_threshold

  - id: consensus
    name: Consensus Docking
    description: >
      Only keep poses that both methods agree on (RMSD below threshold).
      Higher confidence predictions with orthogonal validation.
    params:
      - protein_pdb
      - ligand_smiles
      - ntp_type
      - num_poses
      - exhaustiveness
      - box_size
      - rmsd_agreement_threshold
      - min_engines_agree

params:
  # Required inputs
  - name: protein_pdb
    type: file
    description: Receptor structure (PDB format)
    required: true
    file_type: pdb
    preset_type: pdb

  - name: ligand_smiles
    type: string
    description: Ligand SMILES string
    preset_type: ligand

  - name: ntp_type
    type: string
    description: Pre-configured nucleotide template
    enum:
      - dATP
      - dTTP
      - dGTP
      - dCTP
      - ATP
      - UTP
      - GTP
      - CTP

  # Shared parameters
  - name: num_poses
    type: integer
    description: Number of poses per engine
    default: 10
    minimum: 1
    maximum: 50

  # Uni-Dock specific
  - name: exhaustiveness
    type: integer
    description: Uni-Dock search exhaustiveness
    default: 32
    minimum: 1
    maximum: 256

  - name: scoring_function
    type: string
    description: Uni-Dock scoring function
    default: vina
    enum: [vina, vinardo, ad4]

  - name: box_size
    type: integer
    description: Docking box size (Angstroms)
    default: 25
    minimum: 10
    maximum: 100

  # DiffDock specific
  - name: inference_steps
    type: integer
    description: DiffDock inference steps
    default: 20
    minimum: 10
    maximum: 40

  # Filtering thresholds
  - name: affinity_threshold
    type: number
    description: Uni-Dock affinity cutoff (kcal/mol)
    default: -7.0
    minimum: -20.0
    maximum: 0.0

  - name: confidence_threshold
    type: number
    description: DiffDock confidence cutoff
    default: 0.0
    minimum: -10.0
    maximum: 5.0

  # Consensus mode parameters
  - name: rmsd_agreement_threshold
    type: number
    description: Max RMSD (Å) between poses to consider agreement
    default: 2.0
    minimum: 0.5
    maximum: 10.0

  - name: min_engines_agree
    type: integer
    description: Minimum engines that must agree (1 or 2)
    default: 2
    minimum: 1
    maximum: 2

enabled: true
experimental: false