| --- |
| license: other |
| license_name: source-specific-data-licenses |
| license_link: https://huggingface.co/datasets/kevinlu4588/SimpleFoldData/blob/main/ATTRIBUTION.md |
| language: |
| - en |
| tags: |
| - protein |
| - protein-structure |
| - biology |
| - simplefold |
| pretty_name: SimpleFoldData |
| --- |
| |
| # SimpleFoldData |
|
|
| An independently curated protein-structure dataset. The primary pool now combines |
| **[AFDB-1.6M](https://huggingface.co/datasets/timodonnell/afdb-1.6M)** with experimental |
| PDB chains initially released before 2020-05-01. The target is **1,000,000 distinct |
| sequences with verified coordinates**, preferring PDB for exact duplicates. |
|
|
| **Status: build in progress.** AFDB bulk download and validation are running. |
| Final selection, coordinate packing, and public upload are queued after both |
| source collection jobs succeed. ESM-C 6B production embeddings are not yet queued. |
|
|
| ## Selection and verification |
|
|
| AFDB source revision: `a7ededeb7caeaef3892f40f2e4df3bb9236b02f8`. |
| The source selects one representative per AFDB v4 structural cluster, with an |
| upstream sequence-length limit of 2,048 residues. It is not Apple's exact AFESM |
| selection. Original source cluster and sequence-cluster labels are retained; |
| no joint structural reclustering of PDB and AFDB is claimed. |
|
|
| Every downloaded Parquet file is checked against its source SHA-256. Prediction |
| records must have canonical sequences, complete N/CA/C backbones, finite atom |
| coordinates, sequence/coordinate identity, and recomputed mean pLDDT >80. |
| Experimental PDB chains retain full entity sequences and missing-residue indices; |
| at least 80% of residues must have observed N/CA/C backbone atoms. |
|
|
| The final pool includes eligible unique PDB sequences first, then fills to the |
| target with AFDB records in deterministic seed-17 sequence-hash order. It is sorted |
| by sequence length and hash. Aliases are retained separately. Final selected |
| coordinate bytes are rechecked against their recorded SHA-256 before packing. |
|
|
| Earlier Apple source catalogs, SwissProt candidates and AFESM work are preserved |
| as supplementary sources, outside this primary AFDB/PDB selection. Existing files |
| under `swissprot/` are not the final selected release. |
|
|
| The final source-pool selection must pass sequence/coordinate identity checks, |
| exact deduplication, and count reconciliation. This is a general-purpose data |
| source; no benchmark-specific contamination exclusions are claimed. Apply |
| exclusions for your chosen evaluation set before training for that benchmark. |
|
|
| This repository is not affiliated with or endorsed by Apple. See |
| [ATTRIBUTION.md](ATTRIBUTION.md) for sources and source-specific licenses. |
|
|
| ## Reusable sequence embeddings |
|
|
| ESM-C 6B embeddings are being added as a separate, sequence-hash-addressed cache. |
| The planned representation is the final post-layer-normalization hidden state, |
| one 2,560-dimensional BF16 vector per residue, with special tokens removed. |
| Model revision, tensor shape, full input sequence identity, and computation |
| provenance accompany the cache. Sequences are embedded once after exact |
| deduplication. Long sequences are retained in the structure collection and |
| receive an explicit embedding status; they are never silently cropped. |
|
|
| ## Live progress |
|
|
| Updated 2026-10-14T13:03:54+00:00. Coordinate-qualified candidates before deduplication: **1,671,219**. Final selected unique sequences: **1,000,000**. |
|
|
| [Detailed progress and job status](reports/progress.md) · [Machine-readable status](reports/progress.json) · [HTML dashboard](reports/progress.html) |
|
|
