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.

Abstract
 1. INTRODUCTION
 2. CONNOLLY SURFACE
 3. LOCATING THE EXTERIOR ATOMS OF A PROTEIN
 4. COMPUTING SURFACE PATCHES
  4.1 Rolling blending patch
  4.2 Link blending patch
  4.3 Atomic contact patch
 5. CONCLUSION
 REFERENCES

• Joonghyun Ryu(Voronoi Diagram Research Center, Hanyang University)
• Rhohun Park(Dept. of Industrial Engineering, Hanyang University)
• Deok-Soo Kim(Dept. of Industrial Engineering, Hanyang University)