History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics

Abstract

Prof. Haruki Nakamura, who is the former head of Protein Data Bank Japan (PDBj) and an expert in computational biology, retired from Osaka University at the end of March 2018. He founded PDBj at the Institute for Protein Research, together with other faculty members, researchers, engineers, and annotators in 2000, and subsequently established the worldwide Protein Data Bank (wwPDB) in 2003 to manage the core archive of the Protein Data Bank (PDB), collaborating with RCSB-PDB in the USA and PDBe in Europe. As the former head of PDBj and also an expert in structural bioinformatics, he has grown PDBj to become a well-known data center within the structural biology community and developed several related databases, tools and integrated with new technologies, such as the semantic web, as primary services offered by PDBj.

Keywords: Bioinformatics; Computational biology; Protein Data Bank; Protein Data Bank Japan.

Fig. 1

Changes to PDBj over the years. a Increase in depositions to PDBj. b First group photo of PDBj with Prof. Nakamura in 2003 and c the final one before he retired in 2017

Fig. 2

Snapshots of PDBj’s wwPDB-related activities. a Japanese newspaper article to announce the start of the wwPDB in the Nikkei Newspaper on December 2nd, 2003, shown with permission from the Nihon Keizai Shinbun Inc. The English translation of this article is as follows: “[Protein Data Bank, jointly managed by Japanese, European and American institutions, was established.] Research institutions in Japan, USA, and Europe have jointly established an international data bank for researchers to register protein structural data. The three-dimensional structural data of proteins are useful for elucidating the causes of diseases and developing new drugs. The data analyzed by the institutions in each country will be curated to create an environment that is easy for researchers all over the world. The new data bank is named the “worldwide Protein Data Bank.” It was jointly established by Protein Data Bank Japan, headed by Prof. Haruki Nakamura, and is co-hosted by the Institute for Protein Research, Osaka University, the Research Collaboratory for Structural Bioinformatics in the USA, and the European Bioinformatics Institute in Europe. The three organizations have been collaborating with each other for some time and have decided to conclude this into an agreement for the database and will continue to provide the data free of charge. They also have a plan to standardize the data in order to make it easier for researchers to use the database.” b Photo of the wwPDB PIs at IUCr-2005. c Photo of the third wwPDB-AC meeting (2006) held in Japan

Fig. 3

Prof. Haruki Nakamura at outreach activities organized by PDBj. a A group photo taken at “Science Agora 2016 in Tokyo.” b A snapshot photo taken at “Icho Sai, 2017 at IPR, Osaka University”