| name | saprot |
| description | SaProt — Westlake University structure-aware protein language model using an AA+3Di (Foldseek) structure-aware vocabulary (ICLR 2024). Use when: (1) Structure-informed PLM embeddings for function / fitness / variant tasks, (2) Comparing against ESM-2 with Foldseek SA tokens available, (3) SaProt 1.3B AA-only or SA-token workflows (incl. AFDB/OMG/NCBI-trained checkpoints). Upstream: https://github.com/westlake-repl/SaProt. HF: westlake-repl/SaProt_*. Route via protein-language-model. Related Westlake tools (ProTrek, etc.) — cite separately if used.
|
| license | MIT |
| category | analysis-tools |
| tags | ["SaProt","Westlake","PLM","protein-language-model","Foldseek","3Di","ICLR"] |
| upstream | https://github.com/westlake-repl/SaProt |
| stage | function |
SaProt (Westlake)
Upstream: westlake-repl/SaProt ·
HF: https://huggingface.co/westlake-repl ·
OpenReview: https://openreview.net/forum?id=6MRm3G4NiU
Citation
Su, J. et al. SaProt: Protein Language Modeling with Structure-aware
Vocabulary. International Conference on Learning Representations (ICLR)
(2024). https://openreview.net/forum?id=6MRm3G4NiU
Preprint: https://doi.org/10.1101/2023.10.01.560349
See also docs/references.md.
Analytical thinking
SaProt builds a structure-aware vocabulary: residue tokens combined with
Foldseek 3Di structure tokens (SA tokens), trained on large AF2/PDB-scale
structure–sequence corpora (Westlake REPL lab). Strong on many structure/function
downstream tasks when SA input is available.
Critical upstream caveats:
- 35M / 650M: optimal with SA-token input; frozen AA-only embeddings are
weak — fine-tune if forced to AA-only
- 1.3B (e.g.
SaProt_1.3B_AFDB_OMG_NCBI): works better with both SA and
AA-only modes; metagenome-relevant OMG/NCBI mixing noted in checkpoint names
- SA tokens need structures or Foldseek 3Di — for FASTA→3Di production search
prefer
foldseek + prostt5; SaProt is the PLM, not a search engine
| vs | Prefer SaProt when |
|---|
esm / esmc | Have structures / SA tokens and want structure-aware PLM |
prostt5 | Downstream PLM tasks vs building Foldseek 3Di DBs |
plmsearch | Embedding/finetune model vs remote-homology search wrapper |
Related Westlake releases (ProTrek, Pinal, Evolla, …) — mention only if the
project uses them; keep this skill focused on SaProt.
How to run
Decision tree
Structure-aware protein LM?
├─ AA+3Di SaProt (Westlake) → saprot
├─ Sequence-only modern embeddings → esmc (± esm)
├─ FASTA → Foldseek search → prostt5 + foldseek
└─ Remote homology ranking → plmsearch / deepblast
Related skills
protein-language-model · esmc · esm · prostt5 · foldseek ·
plmsearch · omg · metagenomics-llm · tool-selection
