HADDOCK

BioCodeKb - Bioinformatics Knowledgebase

HADDOCK (High Ambiguity Driven protein-protein DOCKing) is an information-driven flexible docking approach for the modeling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it encodes information from identified or predicted protein interfaces in ambiguous interaction restraints (AIRs) to drive the docking process. HADDOCK can deal with a large class of modelling problems including protein-protein, protein-nucleic acids and protein-ligand complexes, including multi-bodies (N>2) assemblies.


Computational docking is the prediction or modeling of the three-dimensional structure of a biomolecular complex, starting from the structures of the individual molecules in their free, unbound form. The main web interface is user-friendly, requiring only the structures of the individual components and a list of interacting residues as input. Additional web interfaces allow the more advanced user to exploit the full range of experimental data supported by HADDOCK and to customize the docking process. The HADDOCK server has access to the resources of a dedicated cluster and of the e-NMR GRID infrastructure. Therefore, a typical docking run takes only a few minutes to prepare and a few hours to complete.


TARGETED USERS

Any user interested in generating 3D models of biomolecular assemblies based on some experimental information (e.g. mutagenesis, cryo-EM, NMR, XL-MS, SAXS, etc.).


INPUT DATA

  • PDB files of the different partners (up to 6 partners in HADDOCK 2.2)  (required)

  • Ambiguous and/or unambiguous distance/angle restraints between partners residues.

  • Experimentally identified or predicted important residues for the interaction

  • Distance restraints (from NMR, MS, or any technique provide some kind of distance information)

  • Various other NMR-based restraints


OUTPUT DATA

  • 3D models of the complexes as PDB files

  • Statistics and analyses of the generated models (clustering, energies, HADDOCK score, etc.)


The docking protocol of HADDOCK was designed so that the molecules experience varying degrees of flexibility and different chemical environments, and it can be divided in three different stages, each with a defined goal and characteristics:


1. Randomization of orientations and rigid-body minimization

In this initial stage, the interacting partners are treated as rigid bodies, meaning that all geometrical parameters such as bonds lengths, bond angles, and dihedral angles are frozen. The partners are separated in space and rotated randomly about their centres of mass. This is followed by a rigid body energy minimization step, where the partners are allowed to rotate and translate to optimize the interaction. The role of AIRs in this stage is of particular importance. Since they are included in the energy function being minimized, the resulting complexes will be biased towards them.


2. Semi-flexible simulated annealing in torsion angle space

The second stage of the docking protocol introduces flexibility to the interacting partners through a three-step molecular dynamics-based refinement in order to optimize interface packing. It is worth noting that flexibility in torsion angle space means that bond lengths and angles are still frozen. The interacting partners are first kept rigid and only their orientations are optimized. Flexibility is then introduced in the interface, which is automatically defined based on an analysis of intermolecular contacts within a 5Å cut-off. This allows different binding poses coming from it0 to have different flexible regions defined. Residues belonging to this interface region are then allowed to move their side-chains in a second refinement step. Finally, both backbone and side-chains of the flexible interface are granted freedom. The AIRs again play an important role at this stage since they might drive conformational changes.


3. Refinement in Cartesian space with explicit solvent (water)

The final stage of the docking protocol immerses the complex in a solvent shell so as to improve the energetics of the interaction. HADDOCK currently supports water (TIP3P model) and DMSO environments. The latter can be used as a membrane mimic. In this short explicit solvent refinement the models are subjected to a short molecular dynamics simulation at 300K, with position restraints on the non-interface heavy atoms. These restraints are later relaxed to allow all side chains to be optimized.

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