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ProtBert-BFD finetuned on Rosetta 20,40,60AA dataset

This model is finetuned to predict Rosetta fold energy using a dataset of 300k protein sequences: 100k of 20AA, 100k of 40AA, and 100k of 60AA

Current model in this repo: prot_bert_bfd-finetuned-032822_1323


  • 20AA sequences (1k eval set):
    Metrics: 'mae': 0.100418, 'r2': 0.989028, 'mse': 0.016266, 'rmse': 0.127537
  • 40AA sequences (10k eval set):
    Metrics: 'mae': 0.173888, 'r2': 0.963361, 'mse': 0.048218, 'rmse': 0.219587
  • 60AA sequences (10k eval set):
    Metrics: 'mae': 0.235238, 'r2': 0.930164, 'mse': 0.088131, 'rmse': 0.2968

prot_bert_bfd from ProtTrans

The starting pretrained model is from ProtTrans, trained on 2.1 billion proteins from BFD. It was trained on protein sequences using a masked language modeling (MLM) objective. It was introduced in this paper and first released in this repository.

Created by Ladislav Rampasek

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