PROTEIX: An Interactive Database System for Three Dimensional Protein Structures

Tatsuya Akutsu (akutsu@mel.go.jp)

Mechanical Engineering Laboratory
1-2 Namiki, Tsukuba, Ibaraki 305 Japan

Abstract

We have been developing an interactive database system for three dimensional protein structures named PROTEIX. The most important feature of PROTEIX is that it has pattern matching facilities for three dimensional protein structures. For example, such functions as substructure search and alignment of two protein structures are included. As well as such functions, PROTEIX has the following facilities: a mechanism for inputing a file in PDB (Protein Data Bank) data format, an interactive graphic interface, and various pattern matching functions for amino acid sequences (strings).

Currently, PROTEIX is being developed and is used as a workbench for developing pattern matching algorithms. The final target of the system is to be a prototype of a powerful tool for biologists who study relations between amino acid sequences and three dimensional structures of proteins. PROTEIX is implemented on UNIX workstations using C-language. X-window is adopted for the graphic interface.