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Base model: westlake-repl/SaProt_650M_AF2

Task type: pair protein-level 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
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