VDRC (Voronoi Diagram Research Center) - Hanyang Univ. Seoul Korea

We are interested in important, real world problems. Developing theory and algorithms, we always implement to verify their correctness, efficiency, and the robustness before submitting papers.

We have developed software packages (with standard C++) for solving application problems, particularly for structural molecular biology problems, and provide them for free to the research community around the world.

In case of troubles, please send information to jhryu.vdrc(at)gmail.com so that we can help you with the revision.

VoroPack-D NEW

V NEW

A Geometric Library for Disks and Balls Using Voronoi Diagrams and Their Dual Structures.

Papers for users:
- Deok-Soo Kim, Youngsong Cho, and Donguk Kim, Euclidean Voronoi diagram of 3D balls and its computation via tracing edges, Computer-Aided Design, Vol. 37, No. 13, pp. 1412-1424, 2005.
- Deok-Soo Kim, Youngsong Cho, and Kokichi Sugihara, Quasi-worlds and Quasi-operators on Quasi-triangulations, Computer-Aided Design, Vol. 42, Issue 10, pp. 874-888, , 2010.
- Deok-Soo Kim, Youngsong Cho, Kokichi Sugihara, Joonghyun Ryu, and Donguk Kim, Three-dimensional Beta-shapes and Beta-complexes via Quasi-triangulation, Computer-Aided Design, Vol. 42, Issue 10, pp. 911-929, , 2010.

Molecular Geometry Operating System NEW

Geometry Engine Software for Molecular Geometry based on the Voronoi diagram, the quasi-triangulation, and the beta-complex.

Papers for users:
- Deok-Soo Kim, Youngsong Cho, and Donguk Kim, Euclidean Voronoi diagram of 3D balls and its computation via tracing edges, Computer-Aided Design, Vol. 37, No. 13, pp. 1412-1424, 2005.
- Deok-Soo Kim, Youngsong Cho, and Kokichi Sugihara, Quasi-worlds and Quasi-operators on Quasi-triangulations, Computer-Aided Design, Vol. 42, Issue 10, pp. 874-888, , 2010.
- Deok-Soo Kim, Youngsong Cho, Kokichi Sugihara, Joonghyun Ryu, and Donguk Kim, Three-dimensional Beta-shapes and Beta-complexes via Quasi-triangulation, Computer-Aided Design, Vol. 42, Issue 10, pp. 911-929, , 2010.
- Jae-Kwan Kim, Youngsong Cho, Roman A Laskowski, Seong Eon Ryu, Kokichi Sugihara and Deok-Soo Kim, BetaVoid: Molecular Voids via Beta-complexes and Voronoi Diagrams, Proteins: Structure, Functions, and Bioinformatics, Vol.82, No.9, pp.1829-1849, 2014.
- Deok-Soo Kim, Joonghyun Ryu, Hayong Shin, and Youngsong Cho, Beta-decomposition for the Volume and Area of the Union of Three-dimensional Balls and Their Offsets, Journal of Computational Chemistry, Vol. 33, Issue 13, pp. 1252–1273, 2012.
- Deok-Soo Kim, Chong-Min Kim, Chung-In Won, Jae-Kwan Kim, Joonghyun Ryu, Youngsong Cho, Changhee Lee, and Jong Bhak, BetaDock: Shape-priority Docking Method Based on Beta-complex, Journal of Biomolecular Structure & Dynamics, Vol. 29, Issue 1, pp. 219-242, , 2011.

Platform: MS Windows (7, 10) and Linux
Released date: 2019-07-03, Released version: 1.0

V2 (renamed) ~~VDM2D~~

Platform: MS Windows (XP, Vista, 7, 10) and Linux
Released date: 2015-12-18, Released version: 1.0

QuickhullDisk NEW

Dynamic Voronoi Diagram Library NEW

Poretron

Platform: MS Windows (XP, Vista, 7, 10) and Linux
Released date: 2015-12-18, Released version: 1.0

BetaVoid for MS Windows

BetaVoid recognizes molecular voids in the van der Waals surface or the Lee-Richards (solvent accessible) surface and computes their mass properties such the volume and the boundary area. (This program, MS Windows version of BetaVoid, based on the BetaVoid for linux which was developed previously.)

Jae-Kwan Kim, Youngsong Cho, Roman A Laskowski, Seong Eon Ryu, Kokichi Sugihara and Deok-Soo Kim, BetaVoid: Molecular Voids via Beta-complexes and Voronoi Diagrams, Proteins: Structure, Functions, and Bioinformatics, Vol.82, No.9, pp.1829-1849, 2014.

Platform: MS Windows XP, Vista, 7 (32bit)
Released date: 2013-09-10, Released version: 1.0

BetaConcept

BetaConcept is the two-dimensional counterpart of BetaMol and is developed for two reasons. The primary reason is to show the powerful concept and capabilities of BetaMol in the plane so that users of BetaMol can get the idea to use it properly. The other reason is to promote users for identifying applications of the Voronoi diagram of circles, the quasi-triangulation in the plane, and the beta-complex in the plane. (Previously it was called "BetaMol2D")

Jae-Kwan Kim, Youngsong Cho, Donguk Kim and Deok-Soo Kim, Voronoi Diagrams, Quasi-triangulations, and Beta-complexes for Disks in R²: The Theory and Implementation in BetaConcept, Journal of Computational Design and Engineering, Vol.1, No.2, pp.79-87, 2014.

Platform: MS Windows XP, Vista, 7 (32bit)
Released date: 2014-10-15, Released version: 1.1

CardiacVis

BetaMol

BetaMol is a molecular modeling, analysis, and processing software completely based on the theory of the Voronoi diagram, the quasi-triangulation, and the Beta-complex. All functions in BetaMol are based on a single representation of the quasi-triangulation. This version of BetaMol is an intermediate deliverable at the current point of time and upgraded versions will follow.

Youngsong Cho, Jae-Kwan Kim, Joonghyun Ryu, Chung-In Won, Chong-Min Kim, Donguk Kim, and Deok-Soo Kim, BetaMol: a molecular modeling, analysis and visualization software based on the beta-complex and the quasi-triangulation, Journal of Advanced Mechanical Design, Systems, and Manufacturing, Vol.6, Issue 3, pp. 389-403, 2012.

QTFier

QTFier creates a text file containing the quasi-triangulation which is the dual structure of the Voronoi diagram of the spherical balls in the three-dimensional space. The quasi-triangulation file is extremely useful for users who want to analyze the spatial structure among spherical balls such as atoms. Once the file format explained in the report accompanying the software is understood, users can easily do many useful analyses. For the details, please refer to the following papers:

Deok-Soo Kim, Youngsong Cho, Jae-Kwan Kim, and Joonghyun Ryu, QTF: Quasi-triangulation File Format, Computer-Aided Design, Vol.44, Issue 9, pp835-845, 2012.
Deok-Soo Kim, Youngsong Cho, and Kokichi Sugihara, Quasi-worlds and Quasi-operators on Quasi-triangulations, Computer-Aided Design, Vol. 42, Issue 10, pp. 874-888, , 2010.
Deok-Soo Kim, Donguk Kim, Youngsong Cho, and Kokichi Sugihara, Quasi-Triangulation and Interworld Data Structure in Three Dimensions, Computer-Aided Design, Vol. 38, No. 7, pp. 808-819, 2006.

BetaDock

BetaDock is a molecular docking simulation software based on the theory of Beta-complex. We claim that BetaDock is superior to any contemporary docking software while it requires less human intervention. Current version of BetaDock is also an intermediate deliverable of the on-going research.

Deok-Soo Kim, Chong-Min Kim, Chung-In Won, Jae-Kwan Kim, Joonghyun Ryu, Youngsong Cho, Changhee Lee, and Jong Bhak, BetaDock: Shape-priority Docking Method Based on Beta-complex, Journal of Biomolecular Structure & Dynamics, Vol. 29, Issue 1, pp. 219-242, , 2011.

BetaMass

BetaMass calculates the volume of the union of molecular atoms and the area of its boundary based on the theory of beta-complex. We claim that BetaMass is the most precise, fastest software computing these mass properties for van der Waals molecules and their offset models.

Deok-Soo Kim, Joonghyun Ryu, Hayong Shin, and Youngsong Cho, Beta-decomposition for the Volume and Area of the Union of Three-dimensional Balls and Their Offsets, Journal of Computational Chemistry, Vol. 33, Issue 13, pp. 1252–1273, 2012.

BetaSpheC

BetaSpheC calculates the sphericity of a set of spherical balls, particularly for biomolecules, based on the theory of the beta-complex. For the details, please refer to the following paper:

Deok-Soo Kim, Jae-Kwan Kim, Chung-In Won, Chong-Min Kim, Joon Young Park, and Jong Bhak, Sphericity of a protein via the ?-complex, Journal of Molecular Graphics and Modelling, Vol. 28, No. 7, pp. 636-649, 2010.

BetaSuperposer

BetaSuperposer evaluates the similarity between the surfaces of two proteins using the beta-shape that is a geometric structure derived from the Voronoi diagram of molecule.

Jae-Kwan Kim and Deok-Soo Kim, BetaSuperposer: Superposition of Protein Surfaces using Beta-shapes, Journal of Biomolecular Structure & Dynamics, Vol. 30, Issue 6, pp. 684–700, 2012.

BetaVoid

BetaVoid recognizes molecular voids in the van der Waals surface or the Lee-Richards (solvent accessible) surface and computes their mass properties such the volume and the boundary area. Because BetaVoid is based on the beta-complex, its correctness and efficiency are mathematically guaranteed.

VoroQuake

VoroQuake locate the optimal observation site and detect the earthquake signal dead zone very efficiently base on the Voronoi diagram. We believe that the software can be applied to various seismic-related problems.

BetaTunnel

BetaTunnel recognizes tunnels from molecular structure. Because BetaTunnel is based on the Voronoi diagram of atoms in molecules, its correctness and efficiency are mathematically guaranteed.

Demo movie
(Proteasome, PDB accession code: 3SHJ, B. Ref: N. Gallastegui, P. Beck, M. Arciniega, R. Huber, S. Hillebrand, and M. Groll, Hydroxyureas as Noncovalent Proteasome Inhibitors, Angew.Chem.Int.Ed.Engl, Vol. 51, pp. 247-249, 2012.)

Software