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Molecular surfaces of proteins based on β-shapes and Voronoi diagrams of atoms
Joonghyun Ryu,Rhohun Park,Choel-Hyung Cho,Deok-Soo Kim 한국산업응용수학회 2005 한국산업응용수학회 학술대회 논문집 Vol.- No.-
Given the atomic complex of protein, it is important to understand the interactions among proteins. One of the approaches to the problem is to analyze the geometric structure of a protein because it is known that its geometric structure directly determines the protein functions. The molecular surface of the protein is one of the important geometric structure for the analysis of the protein. This paper presents an algorithm for precisely and efficiently computing the molecular surface of a protein using a proposed geometric construct called ß-shape based on the Voronoi diagram of atoms in the protein. Given the Voronoi diagram of atoms based on the Euclidean distance from the atom surfaces, the proposed algorithm first computes a ß-shape with an appropriate probe. Then, the molecular surface is computed by employing the blending operation on the atomic complex of the protein.
Joonghyun Ryu,Rhohun Park,Deok-Soo Kim 한국산업경영시스템학회 2005 한국산업경영시스템학회 학술대회 Vol.2005 No.춘계
Given a protein, it is often necessary to study its geometric and physicochemical properties for studying its structure and predicting funtions of a protein. In this case, a connolly surface of a protein plays important roles for these purpose. A protein consists of a set of amino acids and a set of atoms comprise an amino acide. Since an atom can be represented by a hard 3D sphere in van der Waals model, a protein is usually modeled as a set of 3D spheres. In this paper, we present the algorithm for computing a connolly surface using Euclidean Voronoi diagram atoms of a protein. The algorithm initially locates the exterior aotms of a protein where connolly surface patches exist and computes the patches by tracking their boundary curves. Since a Euclidean Voronoi diagram is uniquely defined independent of probe radius different from other geometric structures, the connolly surfaces defined by probes of different radii can be computed without re-computing the Euclidean Voronoi diagram.