README.md

metadata

license: cc-by-4.0
task_categories:
  - text-generation
language:
  - en
tags:
  - protein-structure
  - alphafold
  - structural-biology
size_categories:
  - 10M<n<100M

AFDB-24M — AlphaFold Database Structures with Cluster-Based Splits

A curated subset of ~24 million AlphaFold Database (AFDB) v4 predicted protein structures, stored as sharded Parquet files. Each row contains the raw mmCIF structure text alongside metadata, precomputed cluster IDs, and leakage-resistant train/val/test split assignments.

Dataset Summary

Property	Value
Source	AlphaFold Database v4 (DeepMind / EMBL-EBI)
Total entries	~24,009,002
Shards	12,005 (2,000 entries each)
Format	Apache Parquet, ZSTD compressed (level 12)
Estimated total size	~1.2 TB
Splits	train (98%), val (1%), test (1%)

Selection Criteria

Entries were selected from the public BigQuery table bigquery-public-data.deepmind_alphafold.metadata with the following filters:

Filter	Value	Description
latestVersion	= 4	Only AFDB v4 structures
skip_fragments	true	uniprotStart = 1 AND uniprotEnd = LENGTH(uniprotSequence) — only full-length UniProt models, no fragments
globalMetricValue	>= 70.0	Minimum global mean pLDDT of 70
LENGTH(uniprotSequence)	<= 2048	Maximum sequence length of 2048 residues

The BigQuery query scans ~178 million rows from the AFDB v4 metadata table. After applying the above filters, approximately 30 million entries are returned. These are then further filtered by cluster membership (see below), yielding the final ~24 million entries.

Cluster-Based Filtering

Only entries present in both of the following precomputed cluster files are included:

1. Sequence clusters (AFDB50) — 7-AFDB50-repId_memId.tsv.gz from Steinegger lab AFDB cluster page (Version 3). Groups proteins at 50% sequence identity using Foldseek.

2. Structural clusters — 5-allmembers-repId-entryId-cluFlag-taxId.tsv.gz from the same source. Only entries with cluFlag=2 (structurally clustered) are loaded; fragments, singletons, and sequence-only entries are excluded. This file groups proteins by 3D fold similarity, which is a stricter criterion than sequence identity.

Entries missing from either cluster file are dropped entirely.

Leakage-Resistant Splits

Split assignment uses the structural cluster representative as the hash key, ensuring all proteins sharing a 3D fold land in the same split.

The algorithm:

1. Look up the structural cluster representative ID for each entry
2. Compute h = SHA1("contactdoc-v1" + "::" + cluster_id)
3. Interpret the first 8 bytes as a uint64: u = uint64 / 2^64 → uniform in [0, 1)
4. Assign split:
   • train if u < 0.98
   • val if 0.98 <= u < 0.99
   • test if u >= 0.99

This is fully deterministic — the same cluster ID always maps to the same split across runs.

Schema

Each Parquet file contains a flat table with the following columns:

Column	Type	Description
entry_id	string	AFDB entry ID (e.g., AF-A0A1C0V126-F1)
uniprot_accession	string	UniProt accession (e.g., A0A1C0V126)
tax_id	int64	NCBI taxonomy ID
organism_name	string	Scientific name of the organism
global_plddt	float32	Global mean pLDDT confidence score (70–100)
seq_len	int32	Sequence length in residues
seq_cluster_id	string	AFDB50 sequence cluster representative entry ID
struct_cluster_id	string	Structural cluster representative entry ID
split	string	train, val, or test
gcs_uri	string	Original GCS URI (e.g., gs://public-datasets-deepmind-alphafold-v4/AF-...)
cif_content	string	Complete raw mmCIF file text

File Structure

shard_000000-009999/
  shard_000000.parquet
  shard_000001.parquet
  ...
  shard_009999.parquet
shard_010000-012004
  shard_010000.parquet
  shard_010001.parquet
  ...
  shard_012004.parquet

Each shard contains up to 2,000 rows (one row per protein structure). Files are compressed with ZSTD at level 12, averaging ~100 MB per shard.

Usage

Loading with PyArrow

import pyarrow.parquet as pq

# Read a single shard
table = pq.read_table("shard_000000-009999/shard_000000.parquet")
print(table.schema)
print(f"{len(table)} rows")

# Access a specific column
entry_ids = table["entry_id"].to_pylist()
cif_texts = table["cif_content"].to_pylist()

Loading with Pandas

import pandas as pd

df = pd.read_parquet("shard_000000-009999/shard_000000.parquet")
print(df[["entry_id", "organism_name", "global_plddt", "seq_len", "split"]].head())

Filtering by Split

import pyarrow.parquet as pq
import pyarrow.dataset as ds

dataset = ds.dataset("./", format="parquet")
train = dataset.to_table(filter=ds.field("split") == "train")

Parsing Structures with Gemmi

import gemmi

row = table.to_pydict()
cif_text = row["cif_content"][0]
doc = gemmi.cif.read_string(cif_text)
structure = gemmi.make_structure_from_block(doc.sole_block())
model = structure[0]
chain = model[0]
print(f"{len(chain)} residues")

Data Source and License

• AlphaFold Database structures are provided by DeepMind and EMBL-EBI under CC BY 4.0.
• Cluster files are from the Steinegger lab, based on Foldseek clustering of AFDB v4 (Version 3 clusters).

Citation

If you use this dataset, please cite the AlphaFold Database:

@article{varadi2022alphafold,
  title={AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models},
  author={Varadi, Mihaly and Anyango, Stephen and Deshpande, Mandar and others},
  journal={Nucleic Acids Research},
  volume={50},
  number={D1},
  pages={D439--D444},
  year={2022},
  doi={10.1093/nar/gkab1061}
}

And the AFDB cluster resource:

@article{barrio2024clustering,
  title={Clustering predicted structures at the scale of the known protein universe},
  author={Barrio-Hernandez, Inigo and Yeo, Jimin and Jänes, Jürgen and others},
  journal={Nature},
  volume={622},
  pages={637--645},
  year={2023},
  doi={10.1038/s41586-023-06510-w}
}