Leaderboard · Mutation effect prediction
VenusREM Leaderboard
Snapshot of VenusREM’s standing on ProteinGym Substitution and how it relates to ProtSSN and ProSST within the same model family.
ProteinGym Substitution
As of April 2025, VenusREM ranked 1st on the ProteinGym DMS substitution zero-shot leaderboard (proteingym.org/benchmarks). Aggregates follow ProteinGym’s bias-corrected protocol (e.g. UniProt- and selection-type–aware Spearman), not a plain arithmetic mean over assays.
Official, continuously updated rankings live on ProteinGym. Treat numbers on this page as a project snapshot; always confirm against the public leaderboard before citing competitive claims.
Model family comparison
Conceptual comparison of modalities — not a substitute for ProteinGym’s full baseline table.
| Model | Venue | Primary modality | MSA | Notes |
|---|---|---|---|---|
| ProtSSN | eLife 2025 | Coords + sequence (EGNN / graph) | No | Structure geometry; strong when MSAs are unavailable |
| ProSST | NeurIPS 2024 | Local structure tokens + sequence | Optional (α=0) | Disentangled sequence–structure attention |
| VenusREM | ISMB/ECCB 2025 | Structure PLM + retrieved MSA | Yes (a2m / a3m) | 1st ProteinGym Substitution (2025.04); VenusMutHub |
Notable claims (context)
Approximate Spearman-scale context reported around MSA-enhanced ProSST / VenusREM family releases (~0.518 on ProteinGym-style aggregates in contemporaneous notes). Prefer the paper tables and the live ProteinGym CSV for exact assay-level values.
| Claim | Context | Source |
|---|---|---|
| 1st place, Substitution | ProteinGym zero-shot DMS substitutions | News · 2025.04.19 |
| ~0.518 Spearman (MSA-enhanced) | Family / ProSST news mentions; VenusREM builds on this regime | Release notes · paper |
| VenusMutHub | Complementary mutation-effect hub evaluations | Paper / project updates |
Related resources
- VenusREM overview — method, wet-lab workflow, citation
- Dataset — ProteinGym a2m / a3m homology packs
- VenusFactory2 — browser scoring at venusfactory.bio