pfnet-research/BMI219-2017-ProteinFolding

UCSF BMI219 Deep Learning (2017), Coding example (Prediction of protein folding with RNN and CNN)

Protein secondary structure prediction with cascaded CNN and RNN

This is an example of the application of deep learning to protein secondary structure prediction. This example is based on [1], but some minor modifications are applied.

See commentary.md for a detailed explanation

Dependency

• Chainer
• NumPy
• six

Usage

Retrieve dataset

bash get_data.sh

Train

PYTHONPATH="." python tools/train.py

Reference

[1] Li, Z., & Yu, Y. (2016). Protein Secondary Structure Prediction Using Cascaded Convolutional and Recurrent Neural Networks. arXiv preprint arXiv:1604.07176.