Alexandre Bonvin bio photo

Computational Structural Biology group focusing on dissecting, understanding and predicting biomolecular interactions at the molecular level.

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HADDOCK2.2 manual


A number of tutorial examples are provided in the example directory of HADDOCK 2.2 that will enable you to perform:

protein-dna              : protein-DNA docking (3CRO)
protein-ligand           : protein-ligand docking (Neuraminidase)
protein-peptide-ensemble : example of ensemble-averaged PRE restraints
                           docking with two copies of a peptide not seeing 
                           eachother (multiple binding modes) (sumo-daxx-simc system)
protein-peptide          : protein-peptide docking from an ensemble of three 
                           peptide conformations with increased flexibility
protein-protein          : protein-protein docking from an ensemble of NMR structure 
                           using CSP data (e2a-hpr)
protein-protein-dani     : protein-protein docking from an ensemble of NMR structure 
                           using CSP data (e2a-hpr) and diffusion anisotropy restraints
protein-protein-pcs      : protein-protein docking using NMR PCS restraints 
                           (eps-hot_pcs system)
protein-refine-pcs       : example of single structure water refinement 
                           with NMR PCS restraints
protein-trimer           : three body docking of a homotrimer using bioinformatic 
                           predictions (pdb1qu9)
solvated-docking         : solvated protein-protein docking (barnase-barstar) using 
                           bioinformatic predictions

A step by step description of the basic protein-protein docking example (E2A-HPR) can be found here.

Refer also to the WeNMR web site that contains several HADDOCK-related tutorials and material.