Base model: westlake-repl/SaProt_650M_AF2

Task type: residue-level classification

Label 1 means a protein residue belongs to a small molecule binding cavity, 0 means it doesn't.

Dataset: SaProtHub/Dataset-Binding_Site_Detection-ProteinShake

Model input type: SA(Structure-aware) sequence

Performance (on test set): 0.603 Mcc

LoRA config:

  • r: 8
  • lora_dropout: 0
  • lora_alpha: 16
  • 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: 100
  • batch size: 64
  • precision: 16-mixed
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