ZDOCK: ZDOCK is a widely used protein-protein docking program specifically designed for antibody-antigen interactions. It employs a fast Fourier transform (FFT) algorithm to explore the binding poses of protein complexes.
HADDOCK: HADDOCK (High Ambiguity Driven biomolecular DOCKing) is a flexible docking program that is suitable for modeling antibody-antigen interactions. It allows you to incorporate experimental data and restraints into the docking process.
ClusPro: ClusPro is an online protein-protein docking server that offers a user-friendly interface for docking studies. It can be applied to antibody-antigen docking and provides both rigid-body and flexible docking options.
RosettaAntibody: RosettaAntibody is an extension of the Rosetta suite that focuses on antibody modeling and antibody-antigen docking. It's a powerful tool for high-resolution modeling of antibody-antigen interactions.
PatchDock: PatchDock is a geometry-based docking algorithm that can be used for protein-protein docking, including antibody-antigen complexes. It is known for its ability to handle complex interfaces.
MOE (Molecular Operating Environment): MOE is a comprehensive molecular modeling and simulation software that includes tools for antibody-antigen docking. It offers various algorithms and scoring functions for accurate docking studies.
AutoDock Vina: While AutoDock Vina is primarily designed for small molecule docking, it can also be used for protein-protein docking, including antibody-antigen interactions. It provides a user-friendly interface and is freely available.
Yasara: Yasara is a molecular modeling and simulation package that includes tools for antibody-antigen docking. It features an intuitive interface and various scoring functions.
PyDock: PyDock is a Python-based protein-protein docking program that can be applied to antibody-antigen docking. It uses an energy-based scoring function to predict binding affinities.
SwissDock: SwissDock is an online docking service that can be used for antibody-antigen docking studies. It provides access to the EADock DSS algorithm for protein-protein interactions.