Download - Euclidean Voronoi Diagram of Atoms and Protein Structure Analysis

Euclidean Voronoi Diagram of AtomsEuclidean Voronoi Diagram of Atoms

and Protein Structure Analysisand Protein Structure Analysis

Deok-Soo KimDeok-Soo Kim

([email protected])([email protected])

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)

Voronoi Diagram Research Center, Hanyang University 2

ContentsContents

VD for points and VD for circles

VD for spheres Protein structure via VD DEMO


Voronoi diagram for pointsVoronoi diagram for points


Voronoi diagram for circlesVoronoi diagram for circles

p1

p2

p3

p4

p5

p6

VD(S) VD(S)

Voronoi diagram for 3D spheresVoronoi diagram for 3D spheres


VD(S) – Sphere setVD(S) – Sphere set


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.)


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


Molecule Surface VisualizationMolecule Surface Visualization

Connolly,Connolly, ScienceScience (83) (83)


Type of blending surfaceType of blending surface

Probe

Probe

Rolling blend

Link blend


Example – Blending surfaceExample – Blending surface


Detection of link blendDetection of link blend


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


Docking in a PocketDocking in a Pocket


DEMO, please!!


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


Thank you!Thank you!

See you at Tokyo!!See you at Tokyo!!

[email protected]@hanyang.ac.krhttp://http://

voronoi.hanyang.ac.krvoronoi.hanyang.ac.kr