Bioinformatics is both in molecular biology and computer science. It uses computers to help us understand the molecular biology by collecting, storing, searching, analyzing or sorting information, especially in molecular genetics and the function of protein or other information science. With the coming of post-genome era, the investigation of proteins and genes become more extensive and in-depth, a number of biological databases have been established. Intact and Inparanoid are two in them. This article mainly introduces the two databases: Intact and Inparanoid. Intact is a public database that stores and analyses interactions of protein molecular. It mainly records the method of and experimental binary interaction. And Inparanoid is public eukaryotic ortholog database. It was developed at the Center for Genomics and Bioinformatics to address the need to identify orthologs. This article describes the two databases on the storage structure of information and how to use them in order to further study later.