Worldwide Protein Data Bank
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.
- Company typePrivate
- Founded1971
- HeadquartersPiscataway, United States
- Headcount1–10
- GTM typeB2B
- OfferingSoftware
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.
Worldwide Protein Data Bank firmographics
Firmographics- 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
Worldwide Protein Data Bank industry classification
Industry- 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
Where Worldwide Protein Data Bank is headquartered
LocationHeadquarters
- HQ city
- Piscataway
- HQ country
- United States
- HQ region
- North America
Offices4 records
Markets served
Worldwide Protein Data Bank business model
Business model- GTM type
- B2B
- Offering type
- Software
- Cost components
- Personnel, Technology or R&D, Infrastructure, Operations
Revenue model
- 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
Worldwide Protein Data Bank product offering
Product offeringCore 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
Companies that use Worldwide Protein Data Bank
Customer profileSegments4 records
Ideal customer profiles4 records
Worldwide Protein Data Bank technology and API
TechnologyTechnology focussed Yes
API detail
- Has API
- Yes
- API docs
- API detail
Core technology
AI maturity
App detail
Integration10 records
Feature5 records
Worldwide Protein Data Bank partnerships and signals
Strategic signalPartnerships
Seven partnerships are on record, tiered core.
- PDBc (Protein Data Bank China)coreAssociate 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)coreUS-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)coreEuropean 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)coreJapanese 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)coreCollects 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)coreCollects 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 FoundationcoreNon-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
Worldwide Protein Data Bank competitors and assessment
Company assessmentEmerging 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
Worldwide Protein Data Bank social profiles
Digital presenceWorldwide Protein Data Bank compliance and trust
Trust signalCompliance1 record
Worldwide Protein Data Bank financial estimates
Financial estimateRevenue estimate
Valuation estimate
Worldwide Protein Data Bank leadership team
Management profileNumber of profiles
Worldwide Protein Data Bank subsidiaries and ownership
Company hierarchySubsidiaries6 records
Worldwide Protein Data Bank funding detail
Funding detailFunding overview
Funding rounds
Investors
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Worldwide Protein Data Bank M&A and investment
M&A and investmentM&A
Investments
M&A and investment is available on the Subscription and Enterprise plan.Contact sales →
Frequently asked questions about Worldwide Protein Data Bank
What does Worldwide Protein Data Bank do?
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.
Is Worldwide Protein Data Bank a public or private company?
Worldwide Protein Data Bank is a private company. It is classified as nonprofit foundation owned and is currently operating.
When was Worldwide Protein Data Bank founded?
Worldwide Protein Data Bank was founded in 1971. It employs 1 to 10 people.
Where is Worldwide Protein Data Bank based?
Worldwide Protein Data Bank is headquartered in Piscataway, United States, in the North America region.
How does Worldwide Protein Data Bank make money?
One revenue line is on record: public Good Model.
Who are Worldwide Protein Data Bank's main competitors?
Emerging players on record are AlphaFold DB (DeepMind / EMBL-EBI), GeneCards / MalaCards and MODBASE. Broad incumbents are Ensembl and NCBI GenBank / RefSeq. ChEMBL (EMBL-EBI) is listed as a regional player. Direct peers are UniProt (European Bioinformatics Institute) and CATH / SCOPe.
Does Worldwide Protein Data Bank have an API?
Yes. The OneDep Validation Web Service provides programmatic remote access to wwPDB validation services. It is offered as a Python package installable via pip, with a command-line client (onedep_validate_cli) and Python API. The API supports file upload in multiple formats (PDBx/mmCIF, mmCIF structure factors, NMR chemical shifts, NMR restraints, EM maps in CCP4 format, NMRstar, NEF), initiates validation, polls for completion, and retrieves results (PDF validation reports and XML data). The service is related to but separate from the OneDep deposition system. Developer documentation is at www.wwpdb.org/validation/onedep-validation-web-service-interface.
What industry is Worldwide Protein Data Bank in?
Worldwide Protein Data Bank's product category is Bioinformatics Data Repository. Its primary akta.pro industry code is HLAGAEAL, Data Management, Reporting & Regulatory Submissions for Central Labs, with a secondary code of HLAAAIAA, High-Throughput Screening & Assay Platforms (HTS/HCS, phenotypic screening). Its NAICS code is 519210 and its SIC code is 8731.