Japan is promoting structural genomics/proteomics projects. The first effort was conceptualized back in 1995, and began with the Protein Folds Project and the Structurome Project (the Whole Cell Project) at RIKEN in 1997. Launched in 2002, the National Project on Protein Structural and Functional Analyses (NPPSFA or the "Protein 3000" Project) was organized by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan. Japan has made the analysis of protein structures and functions a top priority, with the Science and Technology Basic Plan, which is formulated every five years and presently indicates that the emphasis will be placed on "proteomics, the elucidation of protein structures or drug sensitive genes, and on new drug development based on this". As a result, NPPSFA has become Japan's biggest life sciences project.

 The project involves two programs and nine research centers: research laboratories at RIKEN (Program for comprehensive studies) and eight centers (Program for focused studies). The basic aim of the project is to obtain deep insight into the biological network by solving over 3000 protein structures and determining the functions of biological and medical importance. The research topics include investigating the three-dimensional structures and molecular functions, elucidating the molecular mechanisms of biologically and medically important phenomena, developing technologies suitable for large-scale structural biology studies, and discovering chemical compounds to control proteins, which would lead to rational drug design. It is estimated that the project results will form the foundations for biological, medical, and pharmaceutical research and will have a critical impact in supporting general life science research today. Strategic utilization of the research results, particularly in industrial applications such as drug development, is highly anticipated.

 A pipeline for high-throughput structure analyses has been established at each research center with the use of large-scale facilities for protein production and three-dimensional structural determinations (the synchrotron radiation facility, SPring-8 and Photon Factory for X-ray crystallography; and nuclear magnetic resonance (NMR) facilities at RIKEN Genomic Sciences Center, Yokohama City University, and Hokkaido University). According to the statistics obtained in October 2005, the project performed some 2,300 structural analyses. Various research techniques, including those for structure determination, NMR techniques (both software and hardware), automated robotic crystallization/observation systems, automated measurements of X-ray diffraction data, and cell-free protein production are being developed so as to achieve high-throughput analyses.