An Integrated Database of Interaction between Human Proteins and Commonly Used Drugs

Finding new drug target proteins is indispensable to design novel drugs. However, not many target proteins of commonly used drugs have been found until now. Therefore, it is important to clarify target proteins of commonly used drugs in order to design novel drugs. Reverse Proteomics Research Institute (REPRORI), that aims at finding new target proteins from 6,000 proteins obtained from the human full-length cDNA clones generated in NEDO FL project [3] by using 800 known commonly used drugs as probes, started a research project in 2002 in order to build a platform for drug design. In this paper, we report a database system that integrates annotation data of proteins and drugs, and interaction data, to support acquiring knowledge for drug design. Currently several databases of interaction between proteins and ligands have been developed [1]. They, however, deal with only limited types of proteins and drugs, and consist of only literature information. Our database, in contrast, collects known information about proteins and drugs comprehensively as well as newly measured interaction data. To get the most out of those comprehensive data, we annotated proteins and drugs intensively, built a flexible searching system and developed a graphical viewer with matrix representation, “BirdsAnts” which can handle mass data. The system, as a whole, enables us to obtain knowledge of the relationship between interactions and features of proteins and drugs. “BirdsAnts” system is described in detail in software demo [2].