The structure determination of protein-protein complexes is a rather tedious and lengthy process, both by NMR and X-ray crystallography. Several methods based on docking to study protein complexes have been well developed over the past few years. Most of these approaches are however not driven by experimental data but based on combination of energetics and shape complementarity. HADDOCK (High Ambiguity Driven proteinÐprotein DOCKing) is an approach that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments or mutagenesis data. This information is introduced as Ambiguous Interaction Restraints (AIRs) to drive the docking process. An AIR is defined as an ambiguous distance between all residues shown to be involved in the interaction. The accuracy of our approach was demonstrated with three molecular complexes. For two of these complexes, for which both the complex and the free protein structures have been solved, NMR titration data were available. Mutagenesis data were used in the last example. In all cases, the best structures generated by HADDOCK, i.e. the structures with the lowest intermolecular energies, were the closest to the published structure of the respective complexes (within 2.0A backbone RMSD).
HADDOCK Homepage http://www.nmr.chem.uu.nl/haddock/
module load haddock/2.1 haddock2.1
For other versions than 2.1, replace 2.1 with the desired version in both commands.
The documentation can be found at http://www.nmr.chem.uu.nl/haddock