Protein secondary Structure Prediction in Deep Learning

PyTorch implementations of protein secondary structure prediction on CB513.

This implementation is based on https://github.com/alrojo/CB513 and https://github.com/jadore801120/attention-is-all-you-need-pytorch.

Dataset

I used CB513 dataset of https://github.com/alrojo/CB513.

sequence length (train)	sequence length (test)

amino acid (train)	amino acid (test)

secondary structure label(train)	secondary structure label (test)

Usage

You can get more infomations by adding -h option.

pssp-nn

python main.py

pssp-transformer

python preprocess.py
python main.py

Acknowledgement

• https://github.com/alrojo/CB513
• https://github.com/jadore801120/attention-is-all-you-need-pytorch
• Li, Zhen; Yu, Yizhou, Protein Secondary Structure Prediction Using Cascaded Convolutional and Recurrent Neural Networks, 2016.
• Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N. Gomez, Lukasz Kaiser, Illia Polosukhin, Attention Is All You Need