EMBL-EBI AlphaFold Protein Structure Database
E200556
The EMBL-EBI AlphaFold Protein Structure Database is a publicly accessible resource providing predicted 3D structures of proteins generated by DeepMind’s AlphaFold system.
All labels observed (1)
| Label | Occurrences |
|---|---|
| EMBL-EBI AlphaFold Protein Structure Database canonical | 1 |
How this entity was disambiguated
This entity first appeared as the object of triple T1793147 — 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: EMBL-EBI AlphaFold Protein Structure Database Context triple: [AlphaFold, hostedOn, EMBL-EBI AlphaFold Protein Structure Database]
-
A.
AlphaFold
AlphaFold is an artificial intelligence system developed by DeepMind that predicts protein 3D structures from amino acid sequences with unprecedented accuracy, revolutionizing structural biology.
-
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.
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.
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E.
NCBI E-utilities API
The NCBI E-utilities API is a set of programmatic web services that allow automated querying, retrieval, and integration of data from NCBI databases such as PubMed.
- 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: EMBL-EBI AlphaFold Protein Structure Database Target entity description: The EMBL-EBI AlphaFold Protein Structure Database is a publicly accessible resource providing predicted 3D structures of proteins generated by DeepMind’s AlphaFold system.
-
A.
AlphaFold
AlphaFold is an artificial intelligence system developed by DeepMind that predicts protein 3D structures from amino acid sequences with unprecedented accuracy, revolutionizing structural biology.
-
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.
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.
-
E.
NCBI E-utilities API
The NCBI E-utilities API is a set of programmatic web services that allow automated querying, retrieval, and integration of data from NCBI databases such as PubMed.
- F. None of above. chosen
Statements (48)
| Predicate | Object |
|---|---|
| instanceOf |
bioinformatics resource
ⓘ
protein structure database ⓘ scientific database ⓘ |
| accessPolicy |
open access
ⓘ
publicly accessible ⓘ |
| computes |
per-residue confidence metrics
ⓘ
predicted local distance difference test (pLDDT) scores ⓘ |
| dataType |
3D coordinates
ⓘ
predicted models ⓘ protein structure ⓘ |
| developedInCollaborationWith | DeepMind ⓘ |
| domain |
bioinformatics
ⓘ
structural biology ⓘ |
| focusesOn |
proteomes of multiple species
ⓘ
reference proteomes ⓘ |
| hasFeature |
API access
ⓘ
confidence score per residue ⓘ downloadable structure files ⓘ search by protein identifier ⓘ visualization of 3D structures ⓘ |
| hasPartner | DeepMind ⓘ |
| hasProvider |
EMBL-EBI
ⓘ
linked to:
European Bioinformatics Institute
|
| hostedAt |
EMBL-EBI Hinxton campus
ⓘ
linked to:
European Bioinformatics Institute
|
| license | open data license ⓘ |
| maintainedBy |
EMBL-EBI
ⓘ
linked to:
European Bioinformatics Institute
|
| operatedBy |
EMBL-EBI
ⓘ
linked to:
European Bioinformatics Institute
European Bioinformatics Institute ⓘ |
| outputFormat |
PDB format
ⓘ
mmCIF format ⓘ |
| predictionAlgorithm |
deep learning
ⓘ
neural networks ⓘ |
| primaryInput | protein sequences ⓘ |
| provides |
predicted protein 3D structures
ⓘ
protein structure models ⓘ |
| relatedTo |
Ensembl
ⓘ
Protein Data Bank ⓘ UniProt ⓘ
linked to:
UniProt protein sequences
|
| supportsUseCase |
comparative modeling
ⓘ
drug discovery research ⓘ functional annotation of proteins ⓘ protein engineering ⓘ protein structure prediction ⓘ structural bioinformatics research ⓘ |
| targetUser |
bioinformaticians
ⓘ
drug discovery researchers ⓘ research scientists ⓘ structural biologists ⓘ |
| usesMethod | AlphaFold ⓘ |
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: EMBL-EBI AlphaFold Protein Structure Database Description of subject: The EMBL-EBI AlphaFold Protein Structure Database is a publicly accessible resource providing predicted 3D structures of proteins generated by DeepMind’s AlphaFold system.
Referenced by (1)
Full triples — surface form annotated when it differs from this entity's canonical label.