Post on 24-Jan-2016
description
Euclidean Voronoi Diagram of AtomsEuclidean Voronoi Diagram of Atoms
and Protein Structure Analysisand Protein Structure Analysis
Deok-Soo KimDeok-Soo Kim
(dskim@hanyang.ac.kr)(dskim@hanyang.ac.kr)
Voronoi Diagram Research CenterVoronoi Diagram Research Center
Department of Industrial EngineeringDepartment of Industrial Engineering
Hanyang University, Seoul, KoreaHanyang University, Seoul, Korea
(http://voronoi.hanyang.ac.kr)(http://voronoi.hanyang.ac.kr)
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ContentsContents
VD for points and VD for circles
VD for spheres Protein structure via VD DEMO
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Voronoi diagram for pointsVoronoi diagram for points
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Voronoi diagram for circlesVoronoi diagram for circles
p1
p2
p3
p4
p5
p6
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VD(S) VD(S)
Voronoi diagram for 3D spheresVoronoi diagram for 3D spheres
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VD(S) – Sphere setVD(S) – Sphere set
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Computation TimeComputation Time
Pentium4 3.0Ghz, 2GB RAM
0
2
4
6
8
10
12
14
0 200 400 600 800 1,000 1,200
Num. of Generators
Com
puta
tion
Tim
e (s
ec.)
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Geometric Model of MoleculeGeometric Model of Molecule
Reentrant Surface
Contact Surface
Accessible Surface
Atom
Probe (Solvent)
Molecular surface = Molecular surface = Reentrant Surface + Contact SurfaceReentrant Surface + Contact Surface
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Molecule Surface VisualizationMolecule Surface Visualization
Connolly,Connolly, ScienceScience (83) (83)
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Type of blending surfaceType of blending surface
Probe
Probe
Rolling blend
Link blend
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Example – Blending surfaceExample – Blending surface
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Detection of link blendDetection of link blend
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Area of molecular surfaceArea of molecular surface
Area of molecular surface = Area of molecular surface = Area of link blendArea of link blend
+ + Area of rolling blendArea of rolling blend + + Area of contact SurfaceArea of contact Surface
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Docking in a PocketDocking in a Pocket
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DEMO, please!!
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Distances between atom groupsDistances 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
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Thank you!Thank you!
See you at Tokyo!!See you at Tokyo!!
dskim@hanyang.ac.krdskim@hanyang.ac.krhttp://http://
voronoi.hanyang.ac.krvoronoi.hanyang.ac.kr