Protein Data Bank
E200553
The Protein Data Bank is a global repository that archives and provides open access to 3D structural data of biological macromolecules such as proteins and nucleic acids.
All labels observed (8)
| Label | Occurrences |
|---|---|
| Protein Data Bank canonical | 3 |
| PDB | 1 |
| PDBe | 1 |
| PDBj | 1 |
| RCSB PDB | 1 |
| Worldwide Protein Data Bank | 1 |
| Worldwide Protein Data Bank consortium | 1 |
| wwPDB | 1 |
How this entity was disambiguated
This entity first appeared as the object of triple T1793144 — resolving that mention is where its identity was fixed. The disambiguator weighed these candidate entities and picked the highlighted one (or “None”, minting a new entity). This is how homonymy is resolved: the same surface form can point to different entities.
NED1
Entity disambiguation (via context triple)
gpt-5-mini-2025-08-07
Target entity: Protein Data Bank Context triple: [AlphaFold, relatedTo, Protein Data Bank]
-
A.
Cambridge Crystallographic Data Centre
The Cambridge Crystallographic Data Centre is a leading research organization that curates and distributes the world’s primary database of small-molecule organic and metal-organic crystal structures for the scientific community.
-
B.
National Center for Biotechnology Information
The National Center for Biotechnology Information (NCBI) is a U.S. government bioinformatics institution that develops and hosts major biological databases and tools for biomedical research.
-
C.
Crystallographic Information Framework
The Crystallographic Information Framework is a standardized data format and ontology used worldwide for representing, exchanging, and archiving crystallographic and related structural science data.
-
D.
IUCrData
IUCrData is an open-access crystallography data journal published by the International Union of Crystallography, focusing on brief reports of crystal structure determinations and related datasets.
-
E.
Global Biodiversity Information Facility
The Global Biodiversity Information Facility (GBIF) is an international open-data infrastructure that provides free access to biodiversity occurrence records from institutions and citizen-science projects worldwide.
- F. None of above. chosen
- G. Unsure - the case is ambiguous/there is not enough information to decide.
NED2
Entity disambiguation (via description)
gpt-5-mini-2025-08-07
Target entity: Protein Data Bank Target entity description: The Protein Data Bank is a global repository that archives and provides open access to 3D structural data of biological macromolecules such as proteins and nucleic acids.
-
A.
Cambridge Crystallographic Data Centre
The Cambridge Crystallographic Data Centre is a leading research organization that curates and distributes the world’s primary database of small-molecule organic and metal-organic crystal structures for the scientific community.
-
B.
National Center for Biotechnology Information
The National Center for Biotechnology Information (NCBI) is a U.S. government bioinformatics institution that develops and hosts major biological databases and tools for biomedical research.
-
C.
Crystallographic Information Framework
The Crystallographic Information Framework is a standardized data format and ontology used worldwide for representing, exchanging, and archiving crystallographic and related structural science data.
-
D.
IUCrData
IUCrData is an open-access crystallography data journal published by the International Union of Crystallography, focusing on brief reports of crystal structure determinations and related datasets.
-
E.
Global Biodiversity Information Facility
The Global Biodiversity Information Facility (GBIF) is an international open-data infrastructure that provides free access to biodiversity occurrence records from institutions and citizen-science projects worldwide.
- F. None of above. chosen
Statements (61)
| Predicate | Object |
|---|---|
| instanceOf |
biological database
ⓘ
nonprofit organization ⓘ open-access database ⓘ scientific data repository ⓘ |
| abbreviation |
PDB
ⓘ
linked to:
Protein Data Bank
|
| accessPolicy |
free of charge
ⓘ
open access ⓘ |
| alsoKnownAs |
wwPDB
ⓘ
linked to:
Protein Data Bank
|
| collaboratesWith | International structural biology community ⓘ |
| countryOfOrigin |
United States
ⓘ
linked to:
United States of America
|
| dataLicense | permissive data-use policy for research and education ⓘ |
| dataType |
NMR restraints
ⓘ
atomic coordinates ⓘ electron microscopy maps (references) ⓘ structure factors ⓘ |
| foundedBy | Brookhaven National Laboratory ⓘ |
| foundedInYear | 1971 ⓘ |
| governedBy | wwPDB governance policies ⓘ |
| hasCitationGuideline | users should cite the PDB and the original structure publication ⓘ |
| hasDepositionSystem | OneDep ⓘ |
| hasFullName |
Worldwide Protein Data Bank
ⓘ
linked to:
Protein Data Bank
|
| hasIdentifierScheme | PDB ID ⓘ |
| hasQualityControl | validation reports for deposited structures ⓘ |
| hasStandard |
PDB file format
ⓘ
PDBx/mmCIF dictionary ⓘ mmCIF format ⓘ |
| headquartersLocation |
United States
ⓘ
linked to:
United States of America
|
| language | English ⓘ |
| maintainedBy |
Worldwide Protein Data Bank consortium
ⓘ
linked to:
Protein Data Bank
|
| memberOrganization |
BMRB
ⓘ
PDB China ⓘ PDBe ⓘ
linked to:
Protein Data Bank
PDBj ⓘ
linked to:
Protein Data Bank
RCSB PDB ⓘ
linked to:
Protein Data Bank
|
| originalLocation | Brookhaven National Laboratory ⓘ |
| primarySubject |
biological macromolecules
ⓘ
nucleic acids ⓘ proteins ⓘ |
| primaryUse |
bioinformatics
ⓘ
computational chemistry ⓘ drug discovery ⓘ molecular modeling ⓘ structural biology research ⓘ |
| stores |
3D structures of nucleic acids
ⓘ
3D structures of proteins ⓘ 3D structures of protein–ligand complexes ⓘ macromolecular complexes ⓘ |
| subjectArea |
biochemistry
ⓘ
bioinformatics ⓘ molecular biology ⓘ structural biology ⓘ |
| supportsExperimentalMethod |
NMR spectroscopy
ⓘ
X-ray crystallography ⓘ cryo-electron microscopy ⓘ electron microscopy ⓘ |
| typicalIdentifierLength | 4 characters ⓘ |
| usedBy |
academic researchers
ⓘ
biotechnology industry ⓘ pharmaceutical industry ⓘ |
| website |
https://www.rcsb.org
ⓘ
https://www.wwpdb.org ⓘ |
How these facts were elicited
The pipeline generated the facts above by prompting gpt-5.1 with this entity's name + description and the instruction below.
Instruction
You are a knowledge base construction expert. Given a subject entity and a description of it, return factual statements that you know for the subject as a JSON list of dictionaries(triples), where keys must be "subject", "predicate" and "object". The number of facts may be very high, between 25 to 50 or more, for very popular subjects. For less popular subjects, the number of facts can be very low, like 5 or 10. # Requirements - If you don't know the subject at all, return an empty list. - If the subject is not a named entity, return an empty list. - Include at least one triple where predicate is "instanceOf". - Do not get too wordy. - Separate several objects into multiple triples with one object.
Input
Subject: Protein Data Bank Description of subject: The Protein Data Bank is a global repository that archives and provides open access to 3D structural data of biological macromolecules such as proteins and nucleic acids.
Referenced by (10)
Full triples — surface form annotated when it differs from this entity's canonical label.
linked to: Protein Data Bank
linked to: Protein Data Bank
linked to: Protein Data Bank
linked to: Protein Data Bank
linked to: Protein Data Bank
linked to: Protein Data Bank
linked to: Protein Data Bank