---
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