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Euclidean Voronoi Diagram of Atoms and Protein Structure Analysis

Euclidean Voronoi Diagram of Atoms and Protein Structure Analysis. Deok-Soo Kim (dskim@hanyang.ac.kr) Voronoi Diagram Research Center Department of Industrial Engineering Hanyang University, Seoul, Korea (http://voronoi.hanyang.ac.kr). Contents. VD for points and VD for circles

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Euclidean Voronoi Diagram of Atoms and Protein Structure Analysis

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  1. Euclidean Voronoi Diagram of Atomsand Protein Structure Analysis Deok-Soo Kim (dskim@hanyang.ac.kr) Voronoi Diagram Research Center Department of Industrial Engineering Hanyang University, Seoul, Korea (http://voronoi.hanyang.ac.kr)

  2. Contents • VDfor points and VD for circles • VD for spheres • Protein structure via VD • DEMO

  3. Voronoi diagram for points

  4. Voronoi diagram for circles

  5. VD(S) Voronoi diagram for 3D spheres

  6. VD(S) – Sphere set

  7. Computation Time Pentium4 3.0Ghz, 2GB RAM

  8. Geometric Model of Molecule Molecular surface = Reentrant Surface + Contact Surface

  9. Molecule Surface Visualization Connolly,Science (83)

  10. Rolling blend Link blend Type of blending surface Probe Probe

  11. Example – Blending surface

  12. Detection of link blend

  13. Area of molecular surface Area of molecular surface = Area of link blend + Area of rolling blend + Area of contact Surface

  14. Docking in a Pocket

  15. DEMO, please!!

  16. Distances between atom groups • between the closest atoms from both groups • these two atoms define a Voronoi face on the separation surface • distances between centers • average : 6.33 • maximum : 41.69 • minimum : 2.58 • distances between surfaces • average : 4.56 • maximum : 39.87 • minimum : 0.94

  17. Thank you! See you at Tokyo!! dskim@hanyang.ac.kr http://voronoi.hanyang.ac.kr

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