Department of Industrial Engineering, Hanyang University, Seoul, Korea

Voronoi Diagram Research Center

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QTDB: Quasi-triangulation Database

Search from QTDB

Please type PDB ID in search field and click the search button on below.
(* Note that you have to install two programs: 1) "Java Runtime Environment"; and 2) "Java 3D" in the last section "Requirements".)

PDB ID :

Ex) Type in a PDB accession code such as "1a2d" (or "1xbb").
(1a2d is "Adipocyte Lipid Binding protein" and 1xbb is "Tyrosine-protein kinase".)

About QTDB

The Voronoi diagram of molecule represent the proximity among the molecule atoms and the quasi-triangulation represents the topology of the Voronoi diagram in the most concise way in the format of the Interworld data structure. Then, the beta-complex and beta-shape, as subsets of the quasi-triangulation, represent the proximity among the molecular atoms within and on the boundary of the molecule, respectively.

Recent observations from Voronoi Diagram Research Center (VDRC) has shown that the beta-complex and beta-shape are very useful for understanding and computing various structural characteristics of biomolecules such as proteins. While the computation of Voronoi diagram is essential, many applications can be easily solved only by the topology information among atoms and therefore we create this data base so that users can freely get such information for his or her uses in applications.

The purpose of QTDB is to provide the quasi-triangulation and the beta-complex data for protein models provided either by Protein Data Bank (PDB) or by individual user. In addition, QTDB provides the interaction interface among domains in each protein where the domain is created by SCOP DB and stored in Astral format.

If one wishes to get these information for PDB proteins, he or she simply needs to enter the PDB ID. Then, the server supplies the related files from the database so that user can freely download to use.

If one wishes to get these information for a new protein, he or she needs to upload the protein model in PDB format. Then, the server computes the Voronoi diagram of the protein and converts it into the quasi-triangulation. In this case, the interaction interface will not be available because the Astral file is not defined.

When the model is queried, the structure is displayed beneath the query panel via a Java applet implemented using Java3D graphics. The graphics software is not intented to be exhaustive in any sense and has a minimum functions to visualize the molecule. One can check both the molecule itself in a few visualization modes and its interaction interaces if one exists.

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