Classify the protein structures through the sequences of amino acid on the Research Collaborators for Structural Bioinformatics Protein Data Bank dataset. We implemented the following deep neural networks:
- 1d CNN without n-gram
- 1d CNN with 4-gram
- GRU with 3-gram
- 1d CNN + GRU with 3-gram
- other experimental DNNs...
To run them, you need these libraries:
- pandas
- numpy
- matplotlib
- sklearn
- Keras
Best result: Achieve 0.88 and 0.84 F1-score on 10 and 34 classes of protein structures using 1d CNN with 4-gram.