README.md

metadata

license: cc-by-4.0
pretty_name: S(H)ARP reference data
tags:
  - biology
  - protein
  - cath
  - tm-vec
  - igem

S(H)ARP reference data

Reference data for S(H)ARP (Streptomyces Hidden Antibiotic Regulated Pathways), iGEM USP-Brazil 2026. The S(H)ARP repository does not ship these files; its scripts/fetch_data.sh and its Colab notebook download them.

File	Contents
sharp-tmvec-cath-v1.0.tar.gz	TM-Vec 2s index of the CATH S95 v4.4.0 domains, unpacks to sharp/data/tmvec_indexes/cath_s95.*
sharp-tmvec-cath-v1.0.tar.gz.sha256	its SHA-256 checksum

Versions

Each change to this repository is a commit. Use a URL pinned to a commit, not to main: it always serves the same files, and the commit's date shows when they were uploaded.

https://huggingface.co/datasets/EdwardNSeven/sharp-data/resolve/<commit>

Use

In the S(H)ARP Colab notebook, set TMVEC_INDEX_SOURCE in Advanced parameters to the URL above. With a local install:

SHARP_DATA_SOURCE=https://huggingface.co/datasets/EdwardNSeven/sharp-data/resolve/<commit> \
    scripts/fetch_data.sh --tmvec-only

Both check the archive against its .sha256 before unpacking it.

How the index was made

• Sequences: cath-domain-seqs-S95-v4_4_0.fa from https://download.cathdb.info/cath/releases/all-releases/v4_4_0/sequence-data/, 73,535 domains (SHA-256 f93265164dc65340feebfbbffb711fe32bf326037c2bb8422f9fa432e2637387).
• Model: the TM-Vec 2s student model, tmvec2_student.pt (SHA-256 fa79c537849f882a805cd583dd1022ed6c927aae55ab8ba80e89b6ad6f1ea76f), from tmvec-bench.
• Command: tmvec2s-search build from S(H)ARP's sharp/tmvec2s_search.py, with sequences over 600 residues split into overlapping windows and pooled (--long pool --overlap 200). One 512-dimension float32 vector per domain.

The S(H)ARP Colab notebook can also rebuild the index from the same sequences (TMVEC_INDEX_SOURCE = build).

License and citation

The index is derived from CATH, which is licensed under the Creative Commons Attribution 4.0 International License.

• CATH: Waman, V. P., et al. (2025). CATH v4.4: major expansion of CATH by experimental and predicted structural data. Nucleic Acids Research, 53(D1), D348–D355. doi:10.1093/nar/gkae1087
• TM-Vec 2s: Keluskar, A., Batra, P., Bezshapkin, V., Morton, J. T., & Zhu, Q. (2026). TM-Vec 2s: Accelerated Protein Remote Homology Detection. bioRxiv. doi:10.64898/2026.02.05.704073
• TM-Vec: Hamamsy, T., et al. (2024). Protein remote homology detection and structural alignment using deep learning. Nature Biotechnology, 42(6), 975–985. doi:10.1038/s41587-023-01917-2