RCSB Protein Data Bank

What RCSB Protein Data Bank does

RCSB Protein Data Bank (RCSB PDB) is the U.S. node of the Worldwide Protein Data Bank (wwPDB) consortium and a non-profit research data resource providing free, open global access to 3D biomolecular structures. Established in 1998 and jointly hosted by Rutgers University and the University of California San Diego (with additional operations at UC San Francisco and the San Diego Supercomputer Center), the organization serves academic and government researchers, pharmaceutical and biotechnology companies, and educators. Its archive contains 256,006 experimentally-determined structures, 391 integrative structures, and 1,062,058 Computed Structure Models sourced from AlphaFold DB and ModelArchive.

The core platform is RCSB.org, a cloud-hosted (AWS) web application that provides deposition (OneDep), search (Advanced Search, Sequence Similarity, 3D Similarity, Chemical Similarity), visualization (Mol* 3D viewer, Sequence Annotations Viewer, Genome View), and analysis (Pairwise Structure Alignment, wwPDB Validation Reports) tools. Programmatic access is delivered through Data and Search APIs with a Python SDK. AI-powered features introduced in 2026 include a 3D Structure Similarity Search and a help-desk ChatBot. The PDBx/mmCIF data standard and the OneDep deposition system are maintained jointly with wwPDB partners PDBe, PDBj, and BMRB.

RCSB PDB has no commercial revenue stream. All data and services are provided at no cost, and operations are funded by U.S. government grants — NSF (DBI-2321666), DOE (DE-SC0019749), and NIH (R01GM157729, covering NCI, NIAID, and NIGMS) — with supplemental compute from the National Energy Research Scientific Computing Center (NERSC). A 2019 funding event raised $34,500,000. The organization is CoreTrustSeal certified and its data has been cited in over one million published research papers.

Name

RCSB Protein Data Bank

Legal name

Research Collaboratory for Structural Bioinformatics Protein Data Bank

Website

https://rcsb.org

Company type

Private

Founded year

1998

Operating status

Operating

Headcount range

11–50 employees

Short description

RCSB Protein Data Bank is the U.S. node of the Worldwide Protein Data Bank, providing free global access to 256,006+ experimentally-determined 3D biomolecular structures and 1M+ AI-predicted models for academic researchers, pharmaceutical companies, and educators. Funded by NSF, DOE, and NIH grants.

Ownership category

akta.pro rank

Headquarters

HQ city

Piscataway

HQ country

United States

HQ region

North America

Offices3 records

Markets served

GTM type

B2B

Offering type

Software

Cost components

Personnel, Technology or R&D, Infrastructure, Operations, Others

Revenue model

1. Government Grants and Funding: RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. Additional support comes from resources of the National Energy Research Scientific Computing Center (NERSC).

Go-to-market motion1 record

Distribution channels5 records

Marketing channels7 records

Core offering

RCSB Protein Data Bank operates the U.S. node of the worldwide Protein Data Bank archive, providing free open-access search, visualization, and analysis tools for experimentally-determined 3D structures of proteins, nucleic acids, and complex assemblies, supplemented by Computed Structure Models from AlphaFold DB and ModelArchive. The service includes the OneDep deposition and annotation system for submitting new structures, the Mol* 3D molecular viewer, wwPDB validation reports, RESTful Data and Search APIs, and the PDB-101 educational portal for training and outreach.

Product overview

RCSB PDB is a research data resource providing access to the Protein Data Bank (PDB) archive of experimentally-determined and computed 3D biomolecular structures. The core platform at RCSB.org offers search, visualization, and analysis tools including Mol* 3D viewer, Sequence Annotations Viewer, and Genome View. Deposition services through OneDep and pdb_extract enable structure submissions. The resource integrates Computed Structure Models from AlphaFold DB and ModelArchive. PDB-101 provides educational materials. All data is freely available with APIs for programmatic access.

Differentiator

Problem solved

Functional benefit

Products and services

• RCSB.org Core Platform Main web platform for accessing, searching, visualizing, and analyzing 3D biomolecular structures from the Protein Data Bank archive, including experimentally-determined structures, integrative structures, and Computed Structure Models. Used by global researchers in academia, government, and pharmaceutical/biotech drug discovery.
• OneDep Deposition and Annotation System Unified deposition and annotation system for submitting 3D macromolecular structure data to the PDB, operating across all wwPDB deposition centers. Used by structural biologists to deposit X-ray, NMR, EM, and integrative structures globally.
• pdb_extract Software tool that extracts and harvests data in PDBx/mmCIF format from structure determination programs and converts PDB files to mmCIF format for deposition preparation, used by structural biologists preparing structures for submission.
• Validate Structures Standalone validation server for checking X-ray, NMR, or EM structures before depositing to the PDB, generating wwPDB Validation Reports assessing structure quality against the archive.
• PDBx/mmCIF Dictionary Resources Information about the PDBx/mmCIF format, dictionaries, and related software tools used by the wwPDB for macromolecular structure data representation and exchange.
• MAXIT Suite Software suite for processing and curating macromolecular structure data, including format translation and consistency checks used in deposition workflows.
• Mol* (MolStar) 3D Viewer Web-based 3D molecular visualization tool for exploring PDB structures and ligand binding sites, accessible from each structure summary page on rcsb.org.
• RCSB Data API and Search API RESTful Web APIs enabling programmatic access to PDB data, structure searches, and bulk data downloads, used by developers and automated pipelines integrating PDB data into external tools and services.
• PDB-101 Educational Resource Educational portal providing training, outreach, and education materials to build and support the PDB user community, including Molecule of the Month, training courses, guide to PDB data, curricula, and molecular art galleries for teaching structural biology.
• Computed Structure Models (CSMs) Predicted protein structure models from AlphaFold DB and ModelArchive, integrated into the PDB archive and accessible alongside experimentally-determined structures, updated with AlphaFold v6 data in April 2026.
• RCSB PDB Help Desk AI Chatbot AI-powered chatbot service for answering questions about structure deposition, biocuration, validation, and PDB policies, providing automated user support to researchers depositing structures.

Quantifiable outcome

• Over 1 million published research papers cite PDB structures
• +1 more outcomes

Named customers3 records

Segments3 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

Yes

API docs

API detail

Core technology

AI maturity

App detail

Integration8 records

AI capability3 records

Feature7 records

Partnerships

Eleven partnerships are on record, tiered core and moderate.

• wwPDB Consortium (PDBe, PDBj, BMRB)coreStrategic or Co-development PartnerRCSB PDB is one of four regional PDB deposition and processing centers (alongside PDBe at EMBL-EBI, PDBj at Osaka University, and BMRB at UC San Diego) that together form the worldwide Protein Data Bank consortium. The consortium ensures uniform data standards, shared deposition systems, and global accessibility of PDB data.
• EMDataResourcecoreStrategic or Co-development PartnerEMDataResource is a federated database for 3DEM maps and models that integrates with RCSB PDB to provide access to cryo-electron microscopy structure data alongside traditional PDB structures.
• Nucleic Acid Knowledgebase (NAKB)coreStrategic or Co-development PartnerNAKB provides a curated knowledgebase for nucleic acid structures that is integrated with RCSB PDB resources.
• PDB-IHM (Integrative/Hybrid Methods)coreStrategic or Co-development PartnerPDB-IHM is an extension of the PDB archive for structures determined using integrative or hybrid methods combining multiple experimental and computational techniques.
• AlphaFold (DeepMind/European Molecular Biology Laboratory)coreTechnology or IntegrationAlphaFold DB provides computationally predicted protein structure models that are integrated into RCSB PDB as Computed Structure Models (CSMs), accessible alongside experimental structures.
• ModelArchivecoreTechnology or IntegrationModelArchive provides computationally predicted protein structure models that are integrated into RCSB PDB as Computed Structure Models (CSMs), accessible alongside experimental structures.
• wwPDB FoundationmoderateStrategic or Co-development PartnerNon-profit foundation supporting the worldwide Protein Data Bank consortium and its mission to maintain open access to structural biology data.
• Rutgers UniversitycoreOthersPrimary institutional host for RCSB PDB core operations, including the Rutgers Artificial Intelligence and Data Science Collaboratory.
• University of California San DiegocoreOthersPartner institution hosting RCSB PDB operations and related research activities.
• San Diego Supercomputer CentercoreOthersPartner organization providing computational infrastructure and expertise for RCSB PDB operations.
• University of California San FranciscomoderateOthersPartner institution contributing to RCSB PDB operations and structural biology research.

Scale indicators8 records

Recent moves6 records

Expansion highlights5 records

Direct peers

• Protein Data Bank in Europe (PDBe): PDBe, operated by EMBL-EBI, is one of the four wwPDB regional data centers alongside RCSB PDB. It serves the same global community of structural biologists with overlapping deposition, validation, search, and visualisation tools for 3D biomolecular structures, making it RCSB PDB's most direct functional peer.
• Protein Data Bank Japan (PDBj): PDBj, hosted at Osaka University, is the third wwPDB regional data center providing parallel deposition, curation, search, and visualisation services for the PDB archive. It mirrors RCSB PDB's mandate under the same consortium governance, serving Japanese and Asia-Pacific researchers.
• AlphaFold DB: AlphaFold DB, developed by DeepMind and EMBL-EBI, hosts computationally predicted protein structures at genome scale. It is both a data source for RCSB PDB's Computed Structure Models and a competing destination for users seeking protein structure information.
• Biological Magnetic Resonance Bank (BMRB): BMRB, the fourth wwPDB partner hosted at UC San Diego, is the primary repository for NMR spectroscopic data on biological macromolecules. It complements RCSB PDB's structural focus and shares governance, deposition tooling (OneDep), and standards through the wwPDB consortium.
• EMDataResource (EMDR): EMDataResource is a federated repository for 3D cryo-electron microscopy (cryo-EM) maps and models that is directly integrated with RCSB PDB. It addresses an overlapping experimental structural biology use case, particularly as cryo-EM becomes a leading structure-determination method.
• ModelArchive: ModelArchive is an open repository for computationally predicted macromolecular models, similar in purpose to AlphaFold DB. RCSB PDB integrates ModelArchive entries as Computed Structure Models, making it a direct data-source peer and partial functional substitute.

Emerging players

• UniProt: UniProt, maintained by EMBL-EBI, SIB, and PIR, is the canonical protein sequence knowledgebase and is cross-referenced from RCSB PDB's Sequence Annotations Viewer. While focused on sequences rather than 3D structures, it is a foundational complementary resource for the same life science community.

Broad incumbents

• NCBI Structure (Molecular Modeling Database): The NCBI Structure resources, including the Molecular Modeling Database (MMDB) and Cn3D viewer, are operated by the US National Center for Biotechnology Information and provide biomolecular structure data and tools to a broad biomedical research audience, with partial overlap to RCSB PDB's scope.

Others

• CATH: CATH is a hierarchical classification of protein domain structures maintained at UCL. It is a complementary structural bioinformatics resource that consumes and classifies RCSB PDB's experimental structures, serving overlapping structural biology users.
• SCOP / SCOPe: SCOP and SCOPe provide a manually curated structural classification of known protein domains, drawing directly on PDB structures. They serve as a downstream classification layer and complementary resource to RCSB PDB's archive.

Market position

Strengths4 records

Weaknesses4 records

Competitive moat6 records

Key risks6 records

Key highlights7 records

Customer concentration

• Xx.com/buildmodels
• YouTubeyoutube.com/user/RCSBProteinDataBank
• Facebookfacebook.com/RCSBPDB
• LinkedInlinkedin.com/company/rcsb-protein-data-bank

Compliance1 record

Revenue estimate

Valuation estimate

Number of profiles

Profiles2 records

Funding overview

Funding rounds1 record

Investors

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M&A

Investments

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Frequently asked questions about RCSB Protein Data Bank