PDBj

What PDBj does

PDBj (Protein Data Bank Japan) is a non-profit academic research infrastructure organization housed at the Institute for Protein Research, Osaka University (since 2000), operating as one of three founding partners of the worldwide Protein Data Bank (wwPDB) consortium alongside RCSB PDB (US) and PDBe (Europe). It serves as the sole designated regional data center for Asia, the Middle East, Oceania, Belarus, and the Russian Federation, processing macromolecular structure depositions and co-maintaining the single global archive of experimentally-determined 3D protein and nucleic acid structures, which as of July 2026 contains more than 255,900 entries.

The platform is organized as a core archive plus an extensive suite of integrated tools: PDBj Mine (search with quick, advanced, and SQL-based interfaces), the OneDep deposition and validation system, Molmil (WebGL molecular viewer), jV (Java viewer), EM Navigator for electron microscopy, Sequence-Navigator, Omokage shape similarity search, Omni Search, and specialized analysis tools (ASH, MAFFTash, HOMCOS, eF-site family, ProMode Elastic, gmfit, NMRToolBox, CRNPRED). Adjacent derived archives include EMPIARj (raw EM images), BSMA (in silico models), XRDa (crystallographic raw data), and DAQ-ScoreDB. Core data standards are PDBx/mmCIF (the community file format) and PDBML (its XML representation), which underwrite semantic interoperability across structural biology.

PDBj operates on a non-commercial, government-funded model. There is no pricing for data access; the entire archive is released under CC0 1.0 Universal Public Domain Dedication, and website content under CC-BY-4.0. Operating funds come from JST-NBDC (grant JPMJND2205) and AMED-BINDS, with supplementary donations routed through the Osaka University Future Fund. Customer segments are academic and government research institutions, pharmaceutical and biotechnology companies engaged in structure-based drug design, and secondary/tertiary educational institutions, all served globally without a sales motion through the pdbj.org portal, FTP/rsync bulk distribution, and community outreach via conferences, newsletters, and social channels.

Name

PDBj

Legal name

Protein Data Bank Japan

Website

https://pdbj.org

Company type

Private

Founded year

2000

Operating status

Operating

Short description

PDBj (Protein Data Bank Japan) is the non-profit Asian and Middle Eastern regional hub of the worldwide Protein Data Bank, co-maintaining the single global archive of 255,900+ 3D macromolecular structures and providing integrated search, deposition, visualization, and analysis tools for academic researchers, pharmaceutical companies, and educators worldwide under government grant funding.

Ownership category

akta.pro rank

Product category

Structural Biology Database

NAICS

Scientific Research and Development Services (5417)

akta.pro primary industry

Database-as-a-Service (DBaaS) Platforms (HDAEAAAN)

akta.pro secondary industry

Reference Data Management (RDM) (HDAEADAE)

Keywords

• Structural biology database
• Macromolecular structure archive
• Protein structure analysis
• Electron microscopy data
• NMR data repository

Headquarters

HQ city

Suita

HQ country

Japan

HQ region

Asia

Offices1 record

Markets served

GTM type

B2B

Offering type

Software

Cost components

Personnel, Technology or R&D, Infrastructure, Operations

Revenue model

1. Government Research Funding: PDBj operates as a non-profit academic infrastructure funded primarily through government research grants. The database is supported by JST-NBDC (JPMJND2205) and AMED-BINDS, providing ongoing operational funding for data curation, system maintenance, and development activities at Osaka University's Institute for Protein Research.
2. Donations: PDBj accepts donations through the Support Fund for Protein Data Bank Japan, positioned as a project of the Osaka University Future Fund. Donations support public relations activities not covered by government research funding.

Pricing tiers

Go-to-market motion1 record

Distribution channels3 records

Marketing channels5 records

Core offering

PDBj (Protein Data Bank Japan) maintains the single global PDB, BMRB, and EMDB archives of macromolecular structures and provides integrated tools for deposition, search, visualization, and analysis of 3D structures of proteins and nucleic acids. It operates as the regional data center for Asia and the Middle East under the worldwide Protein Data Bank (wwPDB) partnership, processing data depositions and distributing the archive under open-access terms.

Product overview

PDBj (Protein Data Bank Japan) is a platform-plus-modules architecture serving as the Asian hub of the worldwide Protein Data Bank (wwPDB) partnership. The core offering is the PDB archive, containing over 255,900 entries of 3D macromolecular structures. The platform provides multiple integrated modules: PDBj Mine serves as the primary search interface with quick, advanced, and SQL-based search capabilities; EM Navigator provides 3D electron microscopy data browsing with cross-search to PDB; molecular viewers (Molmil WebGL viewer, jV Java viewer) enable 3D structure visualization; and specialized tools like Sequence-Navigator, Omokage shape search, and Omni Search support diverse query methods. Data deposition is handled through the unified OneDep system. Derived databases include BSMA (Biological Structure Model Archive), XRDa (Crystallographic Raw Data Archive), and EMPIARj for raw EM images. Additional services span structure analysis tools (ASH, MAFFTash, HOMCOS, eF-site family), NMR analysis (NMRToolBox), and educational offerings (Molecule of the Month, eProtS). All PDB data is freely available under CC0 1.0 Universal Public Domain Dedication.

Differentiator

Problem solved

Functional benefit

Products and services

• PDBj Mine
• OneDep Deposition System
• EM Navigator (EMnavi)
• Molmil WebGL Molecular Viewer
• jV Graphic Viewer
• PDBx/mmCIF Editor
• Sequence-Navigator
• Omokage Search
• Omni Search
• EMPIARj
• BSMA (Biological Structure Model Archive)
• XRDa (Crystallographic Raw Data Archive)
• DAQ-ScoreDB
• NMRToolBox
• HOMCOS
• ProMode Elastic
• Format Conversion Service
• wwPDB/RDF
• Molecule of the Month
• eProtS (electronic Protein Science Training)

Quantifiable outcome

• More than 2 million items downloaded from PDB every day worldwide
• +3 more outcomes

Named customers3 records

Segments3 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

No

API docs

API detail

Core technology

AI maturity

App detail

Feature6 records

Partnerships

Nine partnerships are on record, tiered core and minor.

• wwPDB (Worldwide Protein Data Bank)coreStrategic or Co-development Partner · 1 July 2003wwPDB partnership established in July 2003 with PDBe, PDBj, and RCSB PDB. BMRB joined in 2006 and EMDB in 2021. The international collaboration ensures PDB data is securely stored, expertly managed, and freely available worldwide. All wwPDB partners process data deposition and maintain the single global PDB archive.
• RCSB PDB (Research Collaboratory for Structural Bioinformatics)coreStrategic or Co-development PartnerUS-based partner responsible for PDB and EMDB data from the Americas. Data is exchanged with RCSB PDB, with synchronized releases from all wwPDB centers.
• PDBe (Protein Data Bank in Europe)coreStrategic or Co-development PartnerEuropean-based partner responsible for PDB and EMDB data from Europe (except Belarus and Russian Federation) and Africa. Coordinates data processing and release with other wwPDB partners.
• BMRB (Biological Magnetic Resonance Data Bank)coreStrategic or Co-development PartnerNMR spectroscopy data bank. BMRB handles data from the Americas, Africa, and Europe while BMRBj (BMRB at PDBj) handles data from Asia.
• EMDB (Electron Microscopy Data Bank)coreStrategic or Co-development Partner3D electron microscopy density maps archive. EMDB joined wwPDB in 2021 as full partner, with data processing shared among wwPDB regional centers.
• JST-NBDC (Japan Science and Technology Agency - National Bioscience Database Center)coreOthersPrimary funding support through NBDC program (JPMJND2205). NBDC coordinates bioscience databases in Japan and supports PDBj operations.
• AMED-BINDS (Japan Agency for Medical Research and Development - Building National Infrastructure)coreOthersFunding support for PDBj operations and infrastructure development under the AMED-BINDS program.
• JBI (Japan Alliance for Bioscience Information)minorOthersMulti-institutional alliance for bioscience information in Japan. PDBj is a member organization contributing to coordinated bioscience database efforts.
• DBCLS (Database Center for Life Science)minorOthersJapan-based life science database center. DBCLS collaborates on data standards and interoperability with PDBj services.

Scale indicators8 records

Recent moves6 records

Expansion highlights6 records

Regional players

• DDBJ: DNA Data Bank of Japan — Japanese partner in the international nucleotide sequence collaboration (GenBank/ENA/DDBJ). Sister life science infrastructure organization in Japan with related scientific mandate.
• DBCLS: Database Center for Life Science — Japan-based life science database infrastructure that collaborates with PDBj on data standards and interoperability within the Japanese bioscience ecosystem.

Direct peers

• PDBe: Protein Data Bank in Europe — EMBL-EBI operated wwPDB partner serving Europe and Africa. Direct peer with shared mission, jointly maintaining the single global PDB archive with PDBj and RCSB.
• BMRB: Biological Magnetic Resonance Data Bank — NMR spectroscopy data archive and wwPDB partner. BMRBj (BMRB at PDBj) handles Asia NMR data, making it a tightly integrated operational peer.
• EMDB: Electron Microscopy Data Bank — 3D EM density maps archive that became a full wwPDB partner in 2021. Directly integrated with PDBj's operations including EM Navigator and shared deposition workflows.
• RCSB PDB: Research Collaboratory for Structural Bioinformatics Protein Data Bank — US-based wwPDB partner maintaining the same global PDB archive, responsible for Americas depositions. PDBj's closest functional peer with shared mission, infrastructure, and synchronized releases.

Broad incumbents

• NCBI: National Center for Biotechnology Information operates GenBank and broader biomedical data infrastructure. Functions as an indirect peer through overlapping life science data services and shared scientific user base.
• UniProt: Comprehensive protein sequence database widely used alongside PDB data. Serves an overlapping structural biology and drug discovery audience with complementary sequence information.

Emerging players

• AlphaFold DB: EMBL-EBI hosted database of AI-predicted protein structures. Functions as a complement/competitor to experimentally-determined PDB data, with growing influence on structural biology workflows that PDBj also serves.
• CATH: Protein structure classification database providing hierarchical domain organization of PDB structures. Serves overlapping structural biology users with derived/classification products built atop PDB data.

Market position

Strengths4 records

Weaknesses4 records

Competitive moat5 records

Key risks5 records

Key highlights6 records

Customer concentration

• Xx.com/PDBj_en
• YouTubeyoutube.com/user/PDBjmovie
• Facebookfacebook.com/PDBjapan

Revenue estimate

Valuation estimate

Number of profiles

Profiles1 record

Funding overview

Funding rounds

Investors

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M&A

Investments

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