AlphaFold Protein Structure Database

Assembled from 20 blocks · 1 evidence · 17 related

1. Story
2. The public database, built and hosted by EMBL's European Bioinformatics Institute at the Wellcome Genome Campus in Hinxton, that turned a method into infrastructure. It opened in July 2021 with predicted structures for the human proteome and a set of model organisms, and in late July 2022 was expanded roughly two hundredfold to cover more than 200 million sequences — effectively the whole of UniProt. A 2024 database paper reports coverage of over 214 million protein sequences. Adoption is the part that matters for this Journey: DeepMind and EMBL-EBI report more than three million researchers in over 190 countries using it by late 2025, over a million of them in low- and middle-income countries, and an independent analysis attributes to its users a substantial rise in submissions of novel experimental structures. That last finding is the useful one, because it distinguishes a tool being downloaded from a tool changing what work gets done.
3. Knowledge
4. AlphaFold
5. AlphaFold Protein Structure Database
6. Connections
7. AlphaFold
8. AlphaFold2 is published and the database opens
9. The AlphaFold database expands to over 200 million structures
10. CASP — Critical Assessment of Structure Prediction
11. Google DeepMind
12. John Jumper
13. Deep learning
14. AlphaFold Protein Structure Database
15. AlphaFold2 is assessed blind at CASP14
16. AlphaFold2 is published and the database opens
17. The AlphaFold database expands to over 200 million structures
18. The Nobel Prize in Chemistry recognises protein structure prediction
19. Evidence
20. The database opened in July 2021 with the human proteome and model organisms, expanded on 28 July 2022 to more than 200 million predicted structures covering effectively the whole of UniProt, and is reported in a 2024 database paper as covering over 214 million sequences; the FAQ states that AlphaFold has not been validated for predicting the effects of destabilising point mutations and that its output is a single conformation rather than a sample of a conformational ensemble. V55 verification basis: no EMBL-EBI page was fetched; search results carried the July 2022 two-hundredfold expansion, the 214-million figure and the paper title with attribution to EMBL-EBI, and carried the mutation and single-conformation limitations with attribution to the AlphaFold DB FAQ. The reported size at the July 2021 launch differs between summaries (figures near 300,000 and near 350,000 both appear) and is therefore not asserted. The adoption figures — over three million researchers in more than 190 countries by late 2025, over a million of them in low- and middle-income countries, and an independently analysed rise of over 40% in users' submissions of novel experimental structures — reached this record through secondary reporting of DeepMind and EMBL-EBI communications and require confirmation.