Worldwide Protein Data Bank

What Worldwide Protein Data Bank does

The Worldwide Protein Data Bank (wwPDB) is an international nonprofit consortium established to manage the Protein Data Bank (PDB), the single global archive of experimentally determined 3D structures of proteins, nucleic acids, and complex assemblies, in continuous operation since 1971. The consortium is composed of regional member organizations — RCSB PDB (US, hosted at Rutgers University), PDBe (Europe, hosted at EMBL-EBI), PDBj (Japan), PDBc (China, associate member since 2022) — plus method-specific partners BMRB (NMR data) and EMDB (electron microscopy data). Its core technical platform, the OneDep deposition and annotation system, accepts structure submissions across X-ray crystallography, NMR spectroscopy, 3D cryo-electron microscopy, and hybrid/integrative methods, and applies community-defined validation, biocuration, and remediation workflows before public release. The wwPDB also maintains the canonical PDBx/mmCIF data format standard, the Chemical Component Dictionary (CCD) and Biologically Interesting Molecule Reference Dictionary (BIRD) reference files, a Python-based OneDep Validation API, and multiple archives (PDB Archive, PDB Beta Archive, PDB Versioned Archive, PDB NextGen Archive) accessible via HTTPS, FTP, and rsync protocols with weekly updates.

wwPDB operates under a public-good business model: deposition, validation, biocuration, remediation, and data access are all provided free of charge to the global community with no usage limitations, in compliance with FAIR data principles. The organization is funded through its member institutions and associated government and scientific funding agencies rather than through user fees or commercial monetization of data. Its served user base spans academic structural biology researchers (primary), pharmaceutical and biotechnology companies engaged in structure-based drug design, scientific journals that require deposition as a condition of publication, and students and educators using the archive for training. Distribution is federated across the four regional member sites, with the archive now exceeding 246,000 released entries and over 1TB of stored data. A generational platform transition to extended 12-character PDB IDs and PDBx/mmCIF as the master format is planned for July 2027.

Name

Worldwide Protein Data Bank

Legal name

Worldwide Protein Data Bank

Website

https://wwpdb.org

Company type

Private

Founded year

1971

Operating status

Operating

Headcount range

1–10 employees

Short description

The Worldwide Protein Data Bank (wwPDB) is a nonprofit consortium managing the single global archive of 3D structures of biological macromolecules since 1971, providing free deposition, validation, and public access to structural biology data for academic researchers, pharmaceutical companies, scientific journals, and educators worldwide.

Ownership category

akta.pro rank

Product category

Bioinformatics Data Repository

NAICS

Libraries and Archives (519210), Medical and Diagnostic Laboratories (6215)

SIC

Services-Commercial Physical & Biological Research (8731), Services-Testing Laboratories (8734)

akta.pro primary industry

Data Management, Reporting & Regulatory Submissions for Central Labs (HLAGAEAL)

akta.pro secondary industry

High-Throughput Screening & Assay Platforms (HTS/HCS, phenotypic screening) (HLAAAIAA)

Keywords

• Structural biology data
• Protein structure archive
• Macromolecular data repository
• Crystallographic data validation
• Bioinformatics data standards

Headquarters

HQ city

Piscataway

HQ country

United States

HQ region

North America

Offices4 records

Markets served

GTM type

B2B

Offering type

Software

Cost components

Personnel, Technology or R&D, Infrastructure, Operations

Revenue model

1. Public Good Model: wwPDB operates as a non-profit public good organization. The PDB archive is freely and publicly available to the global community with no limitations on usage. Expert deposition, validation, biocuration, and remediation services are provided at no charge to data depositors worldwide. The organization is funded through member organizations and funding agencies.

Go-to-market motion1 record

Distribution channels3 records

Marketing channels6 records

Core offering

The Worldwide Protein Data Bank (wwPDB) manages the single global archive of experimentally determined 3D structures of proteins, nucleic acids, and complex assemblies, providing free expert deposition, validation, biocuration, and remediation services to the worldwide scientific community. The organization operates the OneDep unified deposition system across all member sites, the wwPDB Validation Service for pre-deposition structure checking, and maintains critical data standards including the PDBx/mmCIF format, Chemical Component Dictionary, and BIRD reference dictionaries.

Product overview

The Worldwide Protein Data Bank (wwPDB) is a consortium managing the single global archive of 3D structural data for biological macromolecules. The organization operates a unified platform centered on the OneDep Deposition System, which provides a common web-based interface for depositing structures across all wwPDB member sites. The platform includes the OneDep Validation API and wwPDB Validation Service for structure validation, and manages critical data standards including the Chemical Component Dictionary (CCD) for small molecules and ligands, the BIRD dictionary for biologically interesting molecules, and the PDBx/mmCIF format as the master archive format. The wwPDB provides free expert deposition, validation, biocuration, and remediation services, supported by community-driven task forces and working groups that develop validation standards for X-ray, NMR, EM, and hybrid methods. The archive infrastructure includes the PDB Archive, PDB Beta Archive (transitioning to extended 12-character IDs), PDB Versioned Archive, and PDB NextGen Archive, with data accessible via multiple protocols including FTP, HTTPS, and rsync.

Differentiator

Problem solved

Functional benefit

Brands

• OneDep: Next generation PDB deposition and annotation system created by wwPDB partners to unify deposition and annotation systems across all wwPDB deposition centers
• Chemical Component Dictionary (CCD)
• BIRD (Biologically Interesting Molecule Reference Dictionary)
• PDB-IHM
• PDBx/mmCIF

Products and services

• OneDep Deposition System

Quantifiable outcome

• 50+ years of continuous operation managing the global structural data archive
• +2 more outcomes

Segments4 records

Ideal customer profiles4 records

Technology focussed Yes

API detail

Has API

Yes

API docs

API detail

Core technology

AI maturity

App detail

Integration10 records

Feature5 records

Partnerships

Seven partnerships are on record, tiered core.

• PDBc (Protein Data Bank China)coreStrategic or Co-development Partner · 1 January 2022Associate member since 2022, based at National Facility for Protein Science in Shanghai associated with Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai Institute for Advanced Immunochemical Studies, and iHuman Institute of ShanghaiTech University.
• RCSB PDB (Research Collaboratory for Structural Bioinformatics Protein Data Bank)coreStrategic or Co-development PartnerUS-based member organization and primary coordinator of wwPDB. Manages deposition systems, validation services, and main archive access. Provides APIs, visualization tools, and educational resources (PDB-101).
• PDBe (Protein Data Bank in Europe)coreStrategic or Co-development PartnerEuropean member organization hosted at EMBL-EBI. Provides rich information about PDB entries, advanced services (PDBePISA, PDBeFold, PDBeMotif), and validation tools.
• PDBj (Protein Data Bank Japan)coreStrategic or Co-development PartnerJapanese member organization providing multilingual access (English, Japanese, Chinese, Korean). Offers advanced querying (PDBj Mine), shape similarity search (Omokage), and visualization (Molmil). Maintains unique archives for computational models (BSM-Arc) and raw diffraction data (XRDa).
• BMRB (Biological Magnetic Resonance Data Bank)coreTechnology or IntegrationCollects NMR data from experiments, capturing assigned chemical shifts, coupling constants, peak lists, and derived annotations (hydrogen exchange rates, pKa values, relaxation parameters). Integrates with PDB depositions for combined NMR entries.
• EMDB (Electron Microscopy Data Bank)coreTechnology or IntegrationCollects 3D volumes and associated information of macromolecular complexes and subcellular structures from electron cryo-microscopy and tomography. Develops resources for searching, data mining, analyzing, validating, and visualizing EM data. Coordinates with PDB for joint depositions.
• wwPDB FoundationcoreStrategic or Co-development PartnerNon-profit foundation supporting the mission and operations of wwPDB as a public good for structural biology data.

Scale indicators5 records

Recent moves6 records

Expansion highlights5 records

Emerging players

• AlphaFold DB (DeepMind / EMBL-EBI): A large-scale database of AI-predicted protein structures hosted at EMBL-EBI. It is comparable because it is a global structural biology data resource that competes with wwPDB as an entry point for structural queries, though it covers predicted rather than experimentally determined structures.
• GeneCards / MalaCards: Integrated databases of human genes and diseases that aggregate annotations from many sources. It is comparable because it surfaces structural biology evidence (including PDB-derived data) to a broad biomedical audience, though as an aggregator rather than a primary structural repository.
• MODBASE: A database of comparative protein structure models maintained at UCSF. It is comparable because it is a public-good structural biology resource that hosts models derived in part from PDB templates, serving overlapping users but with a focus on homology models rather than experimental structures.

Broad incumbents

• Ensembl: A genome database consortium that provides annotated genome data for vertebrates and other species. It is comparable as a non-profit, EMBL-affiliated, publicly accessible reference database in life sciences that serves overlapping research communities and integrates with protein structural resources.
• NCBI GenBank / RefSeq: The US National Center for Biotechnology Information maintains foundational sequence and genomics databases. It is comparable as a large, government-supported, open-access life-sciences data repository with similar public-good governance, curation responsibilities, and integration with wwPDB through protein reference workflows.

Regional players

• ChEMBL (EMBL-EBI): A manually curated chemical-bioactivity database hosted at EMBL-EBI alongside PDBe. It is comparable because it is a non-profit reference data resource that is frequently used alongside PDB structures in drug discovery workflows and shares EMBL-EBI infrastructure and governance with wwPDB's European partner.

Direct peers

• UniProt (European Bioinformatics Institute): The leading comprehensive protein sequence database. It is comparable because it is a non-profit, community-endorsed, FAIR-compliant reference data archive in life sciences that wwPDB explicitly integrates with (via OneDep) and that researchers pair with PDB in structural biology workflows.
• CATH / SCOPe: Hierarchical classification databases of protein domain structures (CATH at UCL; SCOPe at UC Berkeley). They are comparable because they consume and add value on top of PDB data, providing derived structural classifications and serving overlapping structural biology research audiences.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat5 records

Key risks6 records

Key highlights6 records

Customer concentration

• YouTubeyoutube.com/channel/UCgM7zpapumhWHDMV11FIz0Q
• Facebookfacebook.com/pages/Worldwide-PDB/223648640998643
• LinkedInlinkedin.com/company/wwpdb-foundation

Compliance1 record

Revenue estimate

Valuation estimate

Number of profiles

Subsidiaries6 records

Funding overview

Funding rounds

Investors

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M&A

Investments

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Frequently asked questions about Worldwide Protein Data Bank