Extend-NMR: Extending NMR for Functional and Structural Genomics
Partner 8:Bijvoet Center for Biomolecular Research, Utrecht University
People involved:Alexandre M.J.J. Bonvin, Marc van Dijk, Sjoerd de Vries, Rob Kaptein & Rolf Boelens
Website: http://haddock.chem.uu.nl & http://www.nmr.chem.uu.nl/haddock

HADDOCK: High Ambiguity Driven biomolecular DOCKing

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 biomolecular 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, mutagenesis data or bioinformatic predictions. 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 initially demonstrated using NMR titration data for three protein-protein complexes. Since the original 2003 JACS publication, HADDOCK has been extended to deal with a large variety of data and types of complexes and has shown a strong performance in the CAPRI blind docking experiment. Next to protein-protein docking, HADDOCK has been widely applied to the modelling of protein-DNA, protein-RNA, protein- oligosaccharides and protein-ligand complexes. A friendly user interface has been developed within Extend-NMR that provides control on the docking parameters and allows a simple launch of the calculations via the HADDOCK web portal.

A: Manage multiple projects with ease
C: Full control over ALL the settings of a HADDOCK run
B: Convenient setup and control of Ambiguous Interaction Restraints and flexibility
D: Various export capabilities to run your job on your own computational infrastructure or have our servers run it for you (requires a subscription, http://haddock.chem.uu.nl )

HADDOCK Features

  • Support for various experimental restraint type
  • Easy use of diverse biochemical data to drive the docking
  • User-friendly web portal
  • Support for proteins, nucleic acids, oligosaccharides and small ligands
  • Solvated docking
  • Include flexibility during the docking
  • CCPN integrated and scriptable
  • GRID-enabled (haddock.chem.uu.nl/enmr)

Run on our server http://haddock.chem.uu.nl
Run on your own computer infrastructure

  Universiteit Utrecht