NSTI BioNano 2010

On Delaunay simplices containing functional groups

R. Ördög, V. Grolmusz
Eotvos University, Budapest, HU

Keywords: delaunay functional groups protein functionalized nano-particles statistical


The fast growing PDB contains the three-dimensional description of more than 64,000 structures today. The large majority of the data in the PDB are measured by X-ray crystallography by thousands of researchers in millions of work-hours. After we performed a rigorous re-structuring of the whole PDB, we created the RS-PDB database. Three dimensional protein structures are stored and characterized by the spatial coordinates of heavy atoms in the PDB. To measure the empty spaces inside and near the protein we derived a simplicial complex as the Delaunay decomposition of the point set defined by these atoms as points in space. In an earlier work we used the RS-PDB database for finding crystallographically verified ligands in our test-set of 5,757 proteins. Next the tetrahedra, containing the atoms of these ligands were collected, and classified by the atom-types appearing in the corners of the tetrahedra. In our current work we use the same technique, but instead of the ligands, we only examine the functional groups extracted from them. The statistical results derived here, could later be used to design nano-particles binding to certain parts of targeted proteins.
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