| --- |
| license: other |
| license_name: alphafold3-output-terms-of-use |
| license_link: https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md |
| task_categories: |
| - other |
| tags: |
| - biology |
| - protein-structure |
| - alphafold3 |
| - ancestral-sequence-reconstruction |
| - gene-ontology |
| size_categories: |
| - 100K<n<1M |
| --- |
| |
| # afdb — AlphaFold 3 predicted structures for the GO + ASR sequence catalog |
|
|
| Predicted monomer structures for **292,804 unique protein sequences**: 38,934 |
| from a Gene Ontology molecular-function coupling set and 254,182 audited |
| ancestral sequence reconstructions (312 sequences occur in both). The |
| predictions serve as teacher labels for 1,421,494 training pairs; one structure |
| is reused by every pair referencing that exact sequence. |
|
|
| Sequence IDs are `seq_<sha256(sequence)[:20]>`, so a prediction can always be |
| matched back to its exact sequence. |
|
|
| ## Protocol |
|
|
| Stock open-source AlphaFold 3 with **default settings** — no protocol |
| deviations: |
|
|
| | Setting | Value | |
| |---|---| |
| | Code | google-deepmind/alphafold3 v3.0.4 (`c0f97ed`) | |
| | Genetic search | full standard pipeline: UniRef90, MGnify, small BFD, UniProt | |
| | Templates | searched (PDB seqres + mmCIF, `max_template_date` default 2021-09-30) | |
| | Diffusion samples | 5 (default) | |
| | Recycles | 10 (default) | |
| | Model seed | 20260916 | |
| | Databases | AlphaFold 3 paper versions | |
|
|
| Both MSAs AlphaFold 3 builds are retained: the unpaired MSA and the paired |
| (UniProt) MSA. The paired MSA is kept even though every input is a single chain, |
| because AlphaFold 3 featurises it as `msa_all_seq` regardless of chain count and |
| its presence also changes the unpaired crop size — omitting it would not be the |
| standard protocol. |
|
|
| ## Layout |
|
|
| Per shard (590 shards, ≤500 sequences each, grouped by sequence length): |
|
|
| ``` |
| predictions/<band>/<part>.tar predicted structures, confidences, *_data.json |
| msa/<band>/<part>.tar unpaired and paired A3M files |
| ``` |
|
|
| Files are bundled per shard rather than stored loose: 292,804 predictions would |
| otherwise be well over a million objects. |
|
|
| ## Terms of use |
|
|
| These structures are AlphaFold 3 Output and are provided under, and subject to, |
| the [AlphaFold 3 Output Terms of Use](OUTPUT_TERMS_OF_USE.md). See |
| [LEGALLY_BINDING_TERMS_OF_USE.txt](LEGALLY_BINDING_TERMS_OF_USE.txt). Each |
| per-shard archive also carries AlphaFold 3's own `TERMS_OF_USE.md`. |
|
|
| Released openly for non-commercial research. |
|
|
| ## Citation |
|
|
| > Abramson, J. et al. Accurate structure prediction of biomolecular interactions |
| > with AlphaFold 3. *Nature* **630**, 493–500 (2024). |
| > https://doi.org/10.1038/s41586-024-07487-w |
|
|
