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Information-driven modelling of biomolecular complexes.
Alexandre M. J. J. Bonvin
NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Faculty of Science,
Utrecht University, 3584CH, Utrecht, The Netherlands. Email:
With the presently available amount of genetic information, a lot of attention focuses on systems
biology and in particular on biomolecular interactions. Considering the huge number of such
interactions, and their often weak and transient nature, conventional experimental methods such as Xray
crystallography and NMR spectroscopy will not be sufficient to gain structural insight into those. A
wealth of biochemical and/or biophysical data can however easily be obtained for biomolecular
complexes. Combining these data with docking, the process of modeling the 3D structure of a complex
from its known constituents, should provide valuable structural information and complement the
classical structural methods.
We have developed for this purpose a data-driven docking approach called HADDOCK (High
Ambiguity Driven protein–protein DOCKing) ( which is now also
available as web server ( HADDOCK distinguishes itself from ab-initio
docking methods in the fact that it encodes information from identified or predicted protein interfaces in
ambiguous interaction restraints (AIRs) to drive the docking process. Flexibility is accounted for in
different ways during the docking which allows to model (small) conformational changes taking place
during complex formation.
In my talk I will discuss the various sources of data that can be used to map interactions and
illustrate their use in HADDOCK with examples from our laboratory together with results from our
participation to the blind docking experiment CAPRI (Critical Assessment of PRedicted Interactions)
Dominguez C, Boelens R and Bonvin AMJJ (2003). HADDOCK: A protein-protein docking approach based on
biochemical or biophysical information. J Am Chem Soc 125 1731-1737.
van Dijk ADJ, Boelens R and Bonvin AMJJ (2005). Data-driven docking for the study of biomolecular
complexes. FEBS Journal 272 293-312.
van Dijk M, van Dijk ADJ, Hsu V, Kaptein R, Boelens R and Bonvin AMJJ (2006). Information-driven protein-
DNA docking using HADDOCK: it is a matter of flexibility. Nucl. Acids Res. 34, 3317-3325.
de Vries SJ, van Dijk ADJ, Krzeminski,, M van Dijk M, Thureau A, Hsu V, Wassenaar T and Bonvin AMJJ
(2007). HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the
CAPRI targets. Proteins: Struc. Funct. & Bioinformatic, 69, 726-733.
de Vries SJ and Bonvin AMJJ (2008). How proteins get in touch: Interface prediction in the study of
biomolecular complexes. Curr. Pept. and Prot. Research 9, 394-406

abstract-2009-GERM.pdf, 52 Кб, дата создания: 19.09.2009 2:46, (версия 3 / более ранние версии)