tailieunhanh - Báo cáo khoa học: Data-driven docking for the study of biomolecular complexes

With the amount of genetic information available, a lot of attention has focused on systems biology, in particular biomolecular interactions. Con-sidering the huge number of such interactions, and their often weak and transient nature, conventional experimental methods such as X-ray crystal-lography and NMR spectroscopy are not sufficient to gain structural insight into these. A wealth of biochemical and⁄or biophysical data can, however, readily 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 informa-tion and complement the classical structural methods | ềFEBS Journal REVIEW ARTICLE Data-driven docking for the study of biomolecular complexes Aalt D. J. van Dijk Rolf Boelens and Alexandre M. J. J. Bonvin Department of NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University the Netherlands Keywords biomolecular complexes docking interface mapping Correspondence A. M. J. J. Bonvin Department of NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University 3584CH Utrecht the Netherlands Fax 31 0 30 2537623 Tel 31 0 30 2532652 E-mail Website http Received 1 October 2004 revised 5 November 2004 accepted 10 November 2004 With the amount of genetic information available a lot of attention has focused on systems biology in particular biomolecular interactions. Considering the huge number of such interactions and their often weak and transient nature conventional experimental methods such as X-ray crystallography and NMR spectroscopy are not sufficient to gain structural insight into these. A wealth of biochemical and or biophysical data can however readily 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. In this review we discuss and illustrate the various sources of data that can be used to map interactions and their combination with docking methods to generate structural models of the complexes. Finally a perspective on the future of this kind of approach is given. doi Introduction With the available amount of genetic information a lot of attention is focused on systems biology. Here a central question is how do the various biomolecular units work together to fulfil their tasks To answer this question structural information on complexes is needed. Biochemical and biophysical experiments are widely used to gain

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