docking using Kyte-Doolittle-based water preferences
P. Kastritis, K. Visscher, A. V. van Dijk et al.
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–DNA docking using HADDOCK: it is a matter of flexibility
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.
M. V. van Dijk, A. V. van Dijk, Victor Hsu et al.
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limits of what is achievable in protein-DNA docking: Benchmarking HADDOCK's performance
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.
M. V. van Dijk, A. M. J. J. Bonvin
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assemblies by information-driven docking: Introducing the
E. Karaca, A. Melquiond, S. D. de Vries et al.
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Does Surface Conservation Yield? Application to Data-Driven 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.
S. D. de Vries, A. V. van Dijk, A. M. J. J. Bonvin
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