| name | prostt5 |
| description | ProstT5 — bilingual protein language model translating amino-acid sequences and Foldseek 3Di structure tokens (fine-tuned from ProtT5). Use when: (1) Building Foldseek DBs from FASTA via --prostt5-model, (2) Sequence-only structure-aware search without AlphaFold, (3) AA↔3Di representation tasks. Upstream: https://github.com/mheinzinger/ProstT5. HF: Rostlab/ProstT5. Parent ProtT5: Rostlab/prot_t5_xl_uniref50. Route via protein-language-model; production search usually via foldseek.
|
| license | MIT |
| category | analysis-tools |
| tags | ["ProstT5","ProtT5","PLM","protein-language-model","3Di","Foldseek","Rostlab"] |
| upstream | https://github.com/mheinzinger/ProstT5 |
| stage | function |
ProstT5 (ProtT5 → AA ↔ 3Di)
Upstream: mheinzinger/ProstT5 ·
HF: https://huggingface.co/Rostlab/ProstT5 ·
Parent ProtT5: https://huggingface.co/Rostlab/prot_t5_xl_uniref50
Citation
Heinzinger, M. et al. Bilingual language model for protein sequence and
structure. NAR Genom. Bioinform. 6, lqae150 (2024).
https://doi.org/10.1093/nargab/lqae150
ProtT5 / ProtTrans: Elnaggar, A. et al. ProtTrans: Toward Understanding the
Language of Life Through Self-Supervised Learning. IEEE Trans. Pattern Anal.
Mach. Intell. 44, 7112–7127 (2022).
https://doi.org/10.1109/TPAMI.2021.3095381
See also docs/references.md.
Analytical thinking
ProstT5 fine-tunes ProtT5 to translate between amino acids and Foldseek
3Di tokens. In metagenomics the main production path is Foldseek
createdb/easy-search with --prostt5-model: ~400–4000× faster than predicting
full structures before search, but ProstT5-only DBs lack Cα — no TM-score /
LDDT features that need coordinates.
| vs | Prefer ProstT5 when |
|---|
esm | Need 3Di / Foldseek path, not general ESM embeddings |
foldseek (AFDB coords) | Only FASTA available; accept 3Di-only DB limits |
plmsearch | Structure-token search vs PLM embedding homology |
| ColabFold (deferred) | Prefer AFDB / ProstT5+Foldseek over re-folding catalogues |
How to run
foldseek databases ProstT5 weights tmp
foldseek createdb query.fasta queryDB --prostt5-model weights
foldseek easy-search query.fasta targetDB res.m8 tmp --prostt5-model weights
Decision tree
Need structure-aware protein search from FASTA?
├─ Yes, Foldseek production → foldseek + prostt5 weights
├─ AA embeddings only → esm
├─ PLM embedding homology → plmsearch / deepblast
├─ Have AFDB/PDB structures → foldseek (coords)
└─ Classical sequence → mmseqs2 / diamond
Related skills
protein-language-model · foldseek · esm · esmc · saprot ·
plmsearch · deepblast · unicore · metagenomics-llm ·
homology-search · tool-selection
