ProtSSN · Models & benchmarks
Leaderboard
Checkpoint catalog, ProteinGym context for the ensemble result, and selected downstream adoptions. Live Substitution rankings evolve—always check ProteinGym for the current board.
Model variants
Nine EGNN adapters on ESM2 (k = Cα neighbors, h = GNN hidden size).
Params follow the project README. Recommended single checkpoint: k20_h512; ensemble all nine for best reported ProteinGym score.
| Version | Params | Checkpoint |
|---|---|---|
| k10_h512 | 148M | protssn_k10_h512.pt |
| k10_h768 | 160M | protssn_k10_h768.pt |
| k10_h1280 | 184M | protssn_k10_h1280.pt |
| k20_h512 | 148M | protssn_k20_h512.pt · recommended |
| k20_h768 | 160M | protssn_k20_h768.pt |
| k20_h1280 | 184M | protssn_k20_h1280.pt |
| k30_h512 | 148M | protssn_k30_h512.pt |
| k30_h768 | 160M | protssn_k30_h768.pt |
| k30_h1280 | 184M | protssn_k30_h1280.pt |
Bundle download: ProtSSN.zip (all checkpoints, training history, and configs). Hub page: huggingface.co/tyang816/ProtSSN.
ProteinGym
Snapshot from the project README (Dec 2023): ensemble ProtSSN Spearman ≈ 0.449 on ProteinGym v1.0. Compare current baselines on the live board.
| Setting | Metric | Score | Notes |
|---|---|---|---|
| Ensemble ProtSSN | Spearman | ~0.449 | ProteinGym v1.0 · README, Dec 2023 · MSA-free |
| Single model | — | k20_h512 | Recommended default for one-GPU inference |
| Stability sets | DTm / DDG | paper | Structure–stability correlation evaluations |
Honest context: later methods such as VenusREM lead ProteinGym Substitution when MSA retrieval is available. ProtSSN remains a strong MSA-free sequence–structure baseline and a practical end-to-end scorer when alignments are shallow, costly, or undesirable.
Live leaderboard: proteingym.org/benchmarks.
Selected applications
From the ProtSSN README applications table.
| Year | Venue | Application | Reference |
|---|---|---|---|
| 2026 | Nature | Guided single-site mutagenesis (e.g. L349K) in CytoTape monomer redesign | Zheng et al. |
| 2025 | Acta Pharm. Sin. B | Structure-aware zero-shot scorer on 905 small-scale assays (VenusMutHub) | Zhang et al. |
| 2025 | ProteinGym / VenusFactory2 | Zero-shot mutation scoring via leaderboard and web server | VenusFactory2 · arXiv:2603.27303 |