HADDOCK3

HADDOCK3 provides a modular platform for integrative modeling of biomolecular complexes that incorporates experimental data to guide protein-protein docking, refinement, scoring and analysis.

Key Features:

• Modular architecture: The original rigid pipeline has been broken down into a catalogue of independent modules, enabling increased flexibility in modeling workflows.
• Integrative modeling capabilities: HADDOCK3 can incorporate experimental knowledge into physics-based calculations during complex prediction, refinement, scoring and analysis.
• Third-party integrations: The platform has been enriched with powerful analysis tools and integrations with external methods.
• Multiple modeling scenarios: HADDOCK3 can handle multiple integrative modeling scenarios that were not feasible with previous versions of HADDOCK.
• Complementarity to machine learning: HADDOCK3 serves as a physics-based tool to enrich and complement predictions made by machine learning algorithms in the post-AlphaFold era.

Scientific Applications:

• Protein-protein docking: HADDOCK3 guides protein-protein docking using experimental data to model biomolecular complexes.
• Biomolecular complex prediction: The platform models a variety of biomolecular complexes using integrative approaches combining experimental data with physics-based calculations.
• Post-AlphaFold structure refinement: HADDOCK3 enriches and complements predictions from machine learning algorithms with physics-based modeling.

Methodology:

HADDOCK3 uses physics-based calculations for complex prediction, refinement, scoring and analysis, with experimental knowledge incorporated during modeling.