Visibility-based approach to surface detection of tunnels in proteins

Structural properties of proteins substantially influence their reactivity. Thus, the presence of pathways serving for transportation of a small molecule to the protein active site is crucial. These pathways, called tunnels, are defined by their surroundings --- tunnel lining amino acids (or residues). In consequence, studying these amino acids and their properties is tightly connected with protein reactivity. The set of tunnel lining amino acids detected for a given tunnel can differ with respect to selected algorithm for their computation. The criteria for evaluating their biochemical relevance are different as well, as they can depend on various physico-chemical properties. In this paper we firstly present a novel approach to the detection of tunnel lining amino acids. This approach is more robust in comparison with the existing methods. It is based on the visibility of atoms of the amino acids from the tunnel surface, often derived from the Voronoi diagram. Moreover, the detected set of amino acids is further utilized for an automatic detection of the asymmetric tunnel surface. The results are compared with already existing approaches and the benefits are discussed.