3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules

Motivation: Although a large amount of information on the structure, function and properties of biomolecules is becoming available, it is difficult to understand the relationship between them. Thus, we have attempted to create an integrated relational database, search and visualization tool, 3 DinSight, to help researchers to gain insight into their relationship. Results: We have gathered data on the structure, function and properties of biomolecules, and implemented them into a relational database system. The structural data contain sever al subset data such as protein homologues, protein-DNA complex, in oi-del to enable searching within a specific class of data. The functional data include motif sequence and mutation data of proteins. Also, various amino acid properties are implemented as a relational table. The World Wide Web (WWW) interfaces enable users to carry our various kinds of searches among these data. The locations of motif sequences and mutations are automatically mapped on the structure, and visualized in three-dimensional (3D) space by inter-active viewers, VRML (Virtual Reality Modeling Language) and RasMol. In the case of VRML, the mapped 3D objects are hyperlinked to the corresponding document data. Also, amino acid properties, linked with structure, functional and mutation sites, can be displayed as graph plots.