Data Mining Text mining, e.g.: Structures at specific resolution Structures by negative staining Structures by vitrification Mining structural data, e.g.:

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Presentation transcript:

Data Mining Text mining, e.g.: Structures at specific resolution Structures by negative staining Structures by vitrification Mining structural data, e.g.: Segmentation 3D shape recognition Secondary structure recognition Fold modules recognition

Goals Atomic scale model of a cell Atomic models of interacting complexes Conformational dynamics Difficulties Range of size Range of resolution Range of complexity

Towards the atomic model of a cell Wolfgang Baumeister

Segmentation Niels Volkmann Actin mesh & aldolase Volkmann, 2002, JSB 138:123

Atomic models of complexes 15 Å10 Å5 Å Helix- hunter SitusWah Chiu  sheets Helix orientation SCOP: 1.65 released December CATH: 2.5.1: Released January 2004 If no structure available:

Atomic models of complexes Alasdair Steven 10 Å structure of HBV Fitting of FAB

Helix orientation: the fold 3D cryo EM 4.5 Å resolution Mitsuoka et al. J. Struct. Biol. (1999) De Groot et al., J. Mol. Biol (2000) The directionality of the helices was determined by collecting the best-ftting orientations resulting from a search through the 3D experimental map for a large number of  -helical fragments.

How to describe protein motion without sequence and atomic coordinates The 3D continuous object is decomposed into a set of Voronoi cells that approximate its shape and density distribution. The anisotropic elastic network theory allows the thermal fluctuations to be predicted. Ming et al. PNAS (2002) 99: Tama et al. J. Mol. Biol. (2002) 321: 297–305 Scheuring et al. E. Biophys J, 2001