Protein Three Dimensional Structure Prediction on Object Oriented Database

Akira Shimada (
Hideki Takehara (
Kazunori Toma (

Computer Science Department, Asahi Chemical Industry Co., Ltd.
2-1, Samejima, Fuji, Shizuoka 416, Japan


We defined the protein inverse folding problem with an object oriented database and an empirical hydrophobic penalty function, which was derived from the number of residues around each residue in a protein three dimensional structure. Under the database management system, we compiled the known structures of proteins and the evaluation function into one functional database. In order to compare our approach with the methods proposed by other groups, the functional database was applied to the problem of globin family recognition. Although the penalty function itself is simple and non-optimized, it gave considerably good results.