HADDOCK

HADDOCK performs information-driven flexible docking for modeling biomolecular complexes by encoding interface information as ambiguous interaction restraints to drive the docking process.

Key Features:

• Ambiguous Interaction Restraints (AIRs): Encodes biochemical and/or biophysical interaction data such as chemical shift perturbation data from NMR titration experiments or mutagenesis data as ambiguous distances between all residues shown to be involved in the interaction.
• Cryo-EM Data Integration: Integrates cryo-electron microscopy data in the range of 8.5-21 Å resolution, optionally combined with additional interface information such as mutagenesis and hydroxyl radical footprinting data.
• Support for Mixed Molecule Types: Handles protein-protein, protein-nucleic acids, and protein-ligand complexes.
• Additional Experimental Restraints: Supports a wide range of experimental data types to increase modeling accuracy.

Scientific Applications:

• Protein-Protein Complex Modeling: Predicts three-dimensional structures of protein-protein complexes using NMR chemical shift perturbation data or mutagenesis data.
• Cryo-EM-Guided Structure Determination: Generates high-quality interface models of large macromolecular complexes by combining low-resolution cryo-EM maps with atomic structures and other experimental data.
• Integrative Structural Biology: Combines multiple experimental or predictive information sources to increase accuracy of biomolecular complex structure prediction.

Methodology:

HADDOCK uses ambiguous interaction restraints (AIRs) defined as ambiguous distances between all residues shown to be involved in the interaction to drive the docking process, with structures evaluated by intermolecular energies.