Protein secondary structure assignment through Voronoi tessellation

We present a new automatic algorithm, named VoTAP (Voronoi Tessellation Assignment Procedure), which assigns secondary structures of a polypeptide chain using the list of alpha-carbon coordinates. This program uses three-dimensional Voronoi tessellation. This geometrical tool associates with each amino acid a Voronoi polyhedron, the faces of which unambiguously define contacts between residues. Thanks to the face area, for the contacts close together along the primary structure (low-order contacts) a distinction is made between strong and normal ones. This new definition yields new contact matrices, which are analyzed and used to assign secondary structures. This assignment is performed in two stages. The first one uses contacts between residues close together along the primary structure and is based on data collected on a bank of 282 well-refined nonredundant structures. In this bank, associations were made between the prints defined by these low-order contacts and the assignments performed by different automatic methods. The second step focuses on the strand assignment and uses contacts between distant residues. Comparison with several other automatic assignment methods are presented, and the influence of resolution on the assignment is investigated. (C) 2004 Wiley-Liss, Inc.