README.md

metadata

language: protein
tags:
  - protein language model
datasets:
  - BFD
  - Custom Rosetta

ProtBert-BFD finetuned on Rosetta 20AA dataset

This model is finetuned to predict Rosetta fold energy using a dataset of 100k 20AA sequences.

Current model in this repo: prot_bert_bfd-finetuned-032722_1752

Performance

• 20AA sequences (1k eval set):
  Metrics: 'mae': 0.090115, 'r2': 0.991208, 'mse': 0.013034, 'rmse': 0.114165

• 40AA sequences (10k eval set):
  Metrics: 'mae': 0.537456, 'r2': 0.659122, 'mse': 0.448607, 'rmse': 0.669781

• 60AA sequences (10k eval set):
  Metrics: 'mae': 0.629267, 'r2': 0.506747, 'mse': 0.622476, 'rmse': 0.788972

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