SaProtHub/Model-Structural_Similarity-650M

Base model: westlake-repl/SaProt_650M_AF2

Task type: Protein-protein Regression

Structure Similarity Prediction predicts the (aligned) Local Distance Difference Test (LDDT) of the structures given an unaligned pair of proteins. Target values are computed after alignment with TM-align for all pairs of 1000 randomly sampled single-chain proteins.

Dataset: SaProtHub/Dataset-Structural_Similarity-ProteinShake

Model input type: SA(Structure-aware) sequence

Performance (on test set): 0.695 Spearman's ρ

LoRA config:

• r: 8
• lora_dropout: 0.1
• lora_alpha: 8
• target_modules: ["query", "key", "value", "intermediate.dense", "output.dense"]
• modules_to_save: ["classifier"]

Training config:

• optimizer:
  • class: AdamW
  • betas: (0.9, 0.98)
  • weight_decay: 0.01
• learning rate: 5e-4
• epoch: 3
• batch size: 64
• precision: 16-mixed