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Haddock

Predicts docking of candidate proteins against a target protein using the HADDOCK protocol. Returns the best docking pose, all docked models, and a table of docking scores.

Haddock

Quick Start

  1. Prepare candidate and target PDB structures using Load PDB node.
  2. (Optional) Adjust docking configuration parameters as needed.
  3. Connect candidate and target PDBs to the Haddock node and run docking.

Setup Guide

1. Prepare Input Structures

  1. Use the Load PDB node to load candidate and target protein structures.
  2. Ensure only one target PDB is provided (batching not supported for target).

2. Configure Docking Parameters

  1. Optionally edit the TOML configuration for HADDOCK.
  2. Specify interface residues and chains if required.

3. Run Docking

  1. Connect all required inputs and execute the node.
  2. Review outputs: best docking, all dockings, and scores table.

Basic Usage

Standard Docking

  • Dock a single candidate protein against a single target protein.
  • Specify interface residues and chains for precise docking.
  • Use default or custom HADDOCK configuration.

Configuration

Required Inputs

Field Description Type Example
candidate_pdb Candidate protein structure to dock. PDB {"design_0": "..."}
target_pdb Target protein structure to dock against (must be a single PDB). PDB {"target": "..."}
docking_inputs_config HADDOCK configuration parameters in TOML format. STRING see below
target_specs Residue numbers in the target protein defining the binding interface. STRING 1,2,3
candidate_specs Residue numbers in the candidate protein defining the binding interface. STRING 10,11,12
candidate_chains Chains in the candidate protein to consider for docking. STRING A,B
target_chains Chains in the target protein to consider for docking. STRING A
mode Execution mode: MOCK, PROD, or TEST. STRING PROD

Optional Inputs

None

Outputs

Field Description Example
best.pdb Best of the predicted dockings. {"design_0": "..."}
bound.pdb All predicted dockings. {"design_0_model1": "..."}
scores.csv Docking scores table (caprieval statistics). CSV string

Best Practices

Input Preparation

  • Use high-quality, properly formatted PDB files for both candidate and target.
  • Ensure only one target PDB is provided per run.

Docking Configuration

  • Adjust interface residues and chains for more accurate docking.
  • Use TEST mode for quick validation with minimal sampling.

Troubleshooting

Common Issues

  • Multiple target PDBs provided: Only one target protein is supported. Use Load PDB to select a single target.
  • Docking fails or returns empty results: Check that input PDBs are valid and interface residues/chains are correctly specified.

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