/CollagenTransformer

CollagenTransformer: End-to-End Transformer Model to Predict Thermal Stability of Collagen Triple Helices Using an NLP Approach

Primary LanguageJupyter Notebook

CollagenTransformer

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Original paper:

CollagenTransformer: End-to-End Transformer Model to Predict Thermal Stability of Collagen Triple Helices Using an NLP Approach Authors: Eesha Khare, Constancio Gonzalez-Obeso, David L. Kaplan, Markus J. Buehler mbuehler@mit.edu

ACS Biomaterials Science & Engineering https://pubs.acs.org/doi/full/10.1021/acsbiomaterials.2c00737

This repository includes two pretrained models

BERT-based transformer model: https://github.com/lamm-mit/CollagenTransformer/blob/main/CollagenTransformer_ProtBERT_Inference.ipynb

Small transformer model: https://github.com/lamm-mit/CollagenTransformer/blob/main/CollagenTransformer_SmallTransformer_Inference.ipynb

Training and inference

BERT-based transformer model: https://github.com/lamm-mit/CollagenTransformer/blob/main/CollagenTransformer_ProtBERT_training%20and%20inference.ipynb