Solvated protein-DNA docking using HADDOCK

Marc van Dijk, Koen M Visscher, Alexandre M.J.J Bonvin, Panagiotis L. Kastritis

Research output: Contribution to JournalArticleAcademicpeer-review


Interfacial water molecules play an important role in many aspects of protein-DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein-DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein-DNA complexes containing crystallographically-determined water molecules at their interfaces. Our protocol is capable of reproducing the solvation pattern at the interface and recovers hydrogen-bonded water-mediated contacts in many of the benchmark cases. Solvated docking leads to an overall improvement in the quality of the generated protein-DNA models for cases with limited conformational change of the partners upon complex formation. The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein-DNA complexes.

Original languageEnglish
Pages (from-to)51-63
Number of pages13
JournalJournal of Biomolecular NMR
Issue number1
Publication statusPublished - 2013
Externally publishedYes


  • Algorithms
  • Computational Biology
  • DNA
  • Hydrogen Bonding
  • Macromolecular Substances
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Protein Binding
  • Protein Conformation
  • Protein Interaction Mapping
  • Proteins
  • Solvents
  • Water
  • Journal Article
  • Research Support, Non-U.S. Gov't


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