The Protein Data Bank Japan (PDBj, head Prof. Genji Kurisu)*1, operated by the Institute for Protein Research at Osaka University, and the Tohoku Medical Megabank Organization (ToMMo, head Prof. Masayuki Yamamoto)*2 at Tohoku University have jointly developed and launched a new portal as part of PDBj’s services (https://pdbj.org/uniprot/).
The portal not only provides links to genetic variants from the Japanese Multi Omics Reference Panel (jMorp, head Prof. Kengo Kinoshita)*3, developed by ToMMo, but also includes a tool that facilitates easy visualization of these variants on the 3D structure of proteins. Mapping genetic variants to the 3D structure of proteins is typically a complex task, but this new portal significantly simplifies the process.
The portal compiles the 3D structures of proteins registered in the PDB based on their UniProt IDs. It ranks these structures using a scoring system that takes into account factors such as resolution and the coverage of UniProt amino acid sequences for which 3D structural data is available. This enables users to efficiently select and analyze the relevant structures.
See the following link for details.
Terminology
- *1 Protein Data Bank Japan :PDBj head Prof. Genji Kurisu
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URL: https://pdbj.org/
Protein Data Bank Japan (PDBj) was founded in 2000 at the Institute for Protein Research, Osaka University, as an organization responsible for the activities of the Joint Usage and Research Center. For 20 years, it has collected, edited, and registered information on the three-dimensional structures of proteins and nucleic acids from Asia and the Middle East, and in cooperation with the US RCSB, BMRB, and the European PDBe, has been disseminating all data from the University of Osaka to the world as a single internationally unified protein structure database (PDB).
- *2 Tohoku Medical Megabank Organization:ToMMo head Prof. Masayuki Yamamoto
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URL: https://www.megabank.tohoku.ac.jp/
Founded in 2012 with the aim of recovery from the Great East Japan Earthquake and the realization of personalized prevention and medical care, this organization is promoting the Tohoku Medical Megabank Project together with the Iwate Tohoku Medical Megabank Organization at Iwate Medical University. The Tohoku Medical Megabank Project has been developing a biobank that has collected samples and information by conducting a resident cohort survey and a three-generation cohort survey on 150,000 people since 2013. In addition, the organization is developing a system and building a database so that the samples and information from the biobank can be utilized by both industry and academia. Since 2015, the Japan Agency for Medical Research and Development (AMED) has been the research support organization for this project.
- *3 Japanese Multi Omics Reference Panel:jMorp head Prof. Kengo Kinoshita
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URL: https://jmorp.megabank.tohoku.ac.jp/
The Japanese Multi-Omics Reference Panel (jMorp) is a website operated by the Tohoku Medical Megabank Organization (ToMMo) at Tohoku University that analyzes genome and omics data from participants in the cohort study of the Tohoku Medical Megabank Project and publishes the resulting statistical data. jMorp was launched in July 2015 as a database to publish the results of metabolomic and proteomic data analysis and has since been updated annually to include genome, transcriptome, metagenomics, and other data.
