HADDOCK

HADDOCK
	High Ambiguity Driven protein-protein DOCKing based on biochemical and/or biophysical information.



Version:	1.3 (June 14th, 2004) (changes)
Authors:	Alexandre Bonvin, Utrecht University
Contact:	Bijvoet Center for Biomolecular Research Padualaan 8, 3584 CH Utrecht, the Netherlands Email: a.m.j.j.bonvin@chem.uu.nl Phone: +31-30-2533859 Fax: +31-30-2537623
HADDOCK online: http://www.nmr.chem.uu.nl/haddock HADDOCK discussion list: http://groups.yahoo.com/group/haddock-discuss Publications: When using HADDOCK cite: Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin (2003). HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information. J. Am. Chem. Soc. 125, 1731-1737. The use of residual dipolar couplings in HADDOCK is described in: A.D.J. van Dijk, D. Fushman and A.M.J.J. Bonvin (2005) "Various strategies of using residual dipolar cou plings in NMR-driven protein docking: Application to Lys48-linked di-ubiquitin and validation agains t 15N-relaxation data." Proteins: Struc. Funct. & Bioinformatics, 60, 367-381. The use of diffusion anisotropy data in HADDOCK is described in: A.D.J. van Dijk, R. Kaptein, R. Boelens and A.M.J.J. Bonvin "Combining NMR relaxation with chemical shift perturbation data to drive protein-protein docking" J. Biomol. NMR, 34, 237-244 (2006). Our results in CAPRI, the blind docking experiment, are described in (Note that this entire issue of Protein is dedicated to CAPRI): A.D.J. van Dijk, S.J. de Vries, C. Dominguez, H. Chen, H.-X. Zhou and A.M.J.J. Bonvin (2005) "Data-driven docking: HADDOCKs adventures in CAPRI." Proteins: Struc. Funct. & Bioinformatics, 60, 232-238. The following review on data-driven docking is freely available for download: Aalt D.J. van Dijk, Rolf Boelens and Alexandre M.J.J. Bonvin (2005). "Data-driven docking for the study of biomolecular complexes." FEBS Journal, 272, 293-312. Flexible protein-DNA docking using HADDOCK is described in: M. van Dijk, A.D.J. van Dijk, V. Hsu, R. Boelens and A.M.J.J. Bonvin "Information-driven Protein-DNA Docking using HADDOCK: it is a matter of flexibility." Nucl. Acids Res., 34 3317-3325 (2006). Links to HADDOCK-related articles can be found here. Acknowledgments: HADDOCK is derived from ARIA scripts by Michael Nilges and Jens Linge. J.P. Linge, M. Habeck, W. Rieping and M. Nilges (2003). ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics 19, 315-316. The ongoing development of HADDOCK is the result of a team effort and contributions from Cyril Dominguez, Aalt-Jan van Dijk, Sjoerd de Vries and Marc van Dijk are acknowledged.
Please send any suggestions or enquiries to Alexandre Bonvin
... more than fish or software..., discover the "capitaine" ... Copyright © Hergé Moulinsart 2003