Voronoi partitioning is a method for dividing the space around a series of points into cells, each containing a single point. We have applied this technique to protein-ligand X-ray structures, producing sets of tessellating polyhedra each containing a single atom. The method provides information on the primary contacts in the complex � the faces of the polyhedra correspond to primary atom-atom contacts while secondary interactions are automatically excluded. The area of each face also provides an indication of the significance of the corresponding contact.By analysing a large number of contacts from the PDB (over 100 million), we have generated pseudo-interaction potentials for all relevant atom types. These interaction potentials have a wide range of applications, ranging from protein structure validation to interactive structure-based design and protein-ligand docking. We will discuss the methodology, together a validation of the method and several examples of how it can be used in structure-based design.

Voronoi interaction propensities from the PDB - harnessing 100 million non-covalent interactions

244th National Meeting (2012)

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