Deep protein representations enable recombinant protein expression prediction

This repository contains the code developed for the paper "Deep protein representations enable recombinant protein expression prediction".

UniRep sequence representation

Most of the code is originally from the UniRep repository, but has been modified to suit this project. The script is src/unirep_formatter.py.

Training classifiers

Two scripts contains the code for training classifiers to predict protein expression:

• src/train.py: Trains SVM, LR and RF classifiers
• src/train_ann.py: Train ANN classifiers

Presenting results in tables and/or figures

The notebook Figures_and_tables.ipynb show how to generate the figures and tables of the paper. Specifically Figure 2, Figure 3, Table 1 and supplementary material.