Software

HADDOCK
WHISCY
X-plor scripts
DINOSAUR
IRMA


HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information.

J. Am. Chem. Soc. 125, 1731-1737 (2003).

HADDOCK
HADDOCK (High Ambiguity Driven protein-protein 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.
HADDOCK consists of python scripts derived from ARIA written by Michael Nilges and Jens Linge and makes use of CNS as structure calculation software. Additional scripts (csh, awk, perk) and/or third party software are also used to either prepare the data for HADDOCK or analyze the results.

    Note that since HADDOCK is using CNS, all the classical NMR restraints such as NOEs and residual dipolar couplings can be used for docking as well.

On the HADDOCK home page you will find:
  • general information on HADDOCK
  • tools to generate AIR restraint files and to setup projects
  • instructions to obtain HADDOCK
  • links to the various softwares required to run HADDOCK
  • a manual describing the use of HADDOCK
  • a tutorial



Some of my (+-useful...) old X-PLOR scripts.




DINOSAUR.

A set of programs for structure refinement using direct NOE restraints.

Alexandre Bonvin
Department of NMR Spectroscopy
Bijvoet Center for Biomolecular Research, Utrecht University,
The Netherlands.

More info...

  • View DINOSAUR manual (html)
  • Download DINOSAUR manual (PDF)(1.4 Mb)
To obtain IRMA please fill and return the following license agreement.

References:

  • A.M.J.J. Bonvin, R. Boelens and R. Kaptein (1991).
    "Direct NOE refinement of biomolecular structures using 2D NMR data."
    J. Biomol. NMR 1, 305-309
  • A.M.J.J. Bonvin, R. Boelens and R. Kaptein (1994).
    "Time- and ensemble-averaged direct NOE restraints."
    J. Biomol. NMR 4, 143-149.
  • A.M.J.J. Bonvin
    "Determination of biomolecular structures by NMR. Use of relaxation matrix calculations."
    PhD Thesis, Utrecht University (1993) ISBN 90-393-0408-4.



IRMA.

The IRMA procedure calculates distances from experimental NOE spectra with the use of the full relaxation matrix approach.

Rolf Boelens, Alexandre Bonvin
Department of NMR Spectroscopy
Bijvoet Center for Biomolecular Research, Utrecht University,
The Netherlands.

More info...

  • View IRMA2 manual (html)
  • Download IRMA2 manual (PDF)(328 Kb)
To obtain IRMA please fill and return the following license agreement.

References:

  • R. Boelens, T.M.G. Koning and R. Kaptein (1988)
    "Determination of biomolecular structures from proton-proton NOE's using a relaxation matrix approach"
    J. Mol. Structure, 173, 299-311.
  • R. Boelens, T.M.G. Koning, G.A. van der Marel, J.H. van Boom and R. Kaptein (1989)
    "Iterative procedure for structure determination from proton-proton NOE's using a full relaxation matrix approach. Application to a DNA octamer"
    J. Magn. Reson., 82, 290-308.
  • A.M.J.J. Bonvin, J.A.C. Rullmann, R.M.J.N. Lamerichs, R. Boelens and R. Kaptein (1993)
    "Ensemble Iterative Relaxation Matrix Approach: a new NMR refinement protocol applied to the solution structure of crambin."
    PROTEINS: Structure, Function & Genetics 15, 385-400.
  • A.M.J.J. Bonvin, R. Boelens and R. Kaptein (1996)
    "Protein Structures: Relaxation matrix refinement."
    In: Encyclopedia of Nuclear Magnetic Resonance Vol. 6. Eds D.M. Grant and R.K. Harris, John Wiley & Sons, 3801-3811.



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