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A novel and simple hydrophobicity scale derived from the Kyte-Doolittle hydrophobicity scale leads to a performance improvement of around 10% in ranking, cluster quality and water recovery at the interface compared with the statistics-based original solvated docking protocol.
This study extends HADDOCK to deal with DNA flexibility and is able to successfully predict protein (cid:1) DNA complexes from unbound constituents using non-structural experimental data to drive the docking.
The flexible data-driven docking method HADDOCK is able to predict many of the specific DNA conformational changes required to assemble the interface(s) and is the first to readily dock multiple molecules simultaneously, pushing the limits of what is currently achievable in the field of protein–DNA docking.
The interface prediction program WHISCY is presented, which combines surface conservation and structural information to predict protein–protein interfaces and demonstrates the potential of using interface predictions to drive protein–protein docking.
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