The processes of life, mediated by a large variety of proteins, are very complex. Elucidation of these processes through molecular studies of proteins can be achieved by efficient cooperation of researchers in various fields of natural sciences. Another requisite is the establishment of suitable infrastructure that allows close collaborations among scientists across the country. The Institute for Protein Research (IPR) was founded as a joint-use research organization attached to Osaka University to fulfill these needs, and thus to play a central role in protein science in Japan. Emphasis was laid on studies on the structure and function of proteins and their biological significance at the molecular level, as well as investigations at the cellular level. Remarkable progress in the life sciences has been made since the foundation of IPR. Recently, the institute has initiated various projects on protein engineering, structural biology, neurobiology, proteomics, and protein informatics in addition to the traditional activities. Although IPR started as a domestic center, it is now widely recognized as an international center of excellence for protein research. For instance, IPR operates the Worldwide Protein Data Bank (wwPDB) as one of four worldwide centers, mainly covering Asia region. Because of its high standard of scientific activity, it has attracted many researchers from abroad and will continue to do so in the future. IPR will continue to make essential contributions to revealing the structure and function of proteins and their protein networks for the elucidation of life.