beforesunrise710 / prostata Goto Github PK

This repository contains datasets, model code and notebooks used for all experiments in the PROSTATA: Protein Stability Assessment using Transformers paper.

Folders:

• DATA contains the datasets used for PROSTATA training and testing in the format used by the datasets authors. Also the dataset introduced in this article is available here .
• DATASETS contains the same datasets converted to a format used for model training.
• PDB contains the PDB files downloaded during conversion.

Notebooks:

• 00.generate_datasets.ipynb - Process the DATA. folder and generate the DATASETS folder
• 01.test_models_by_folds.ipynb - Test each individual model in the ensemble using5-fold cross validation
• 02.test_models_on_other_datasets_ensemble.ipynb - test the PROSTATA ensemble on various combinations of train and test datasets. Output is logged to the PROSTATA_experiments_pearson.log
• 03.train_final_ensemble.ipynb - train the ensemble on all data for the online tool.
• PROSTATA_tool.ipynb - Colab notebook for PROSTATA. Predict DDG Values for single mutation on user sequence.

Other files:

• PROSTATA_experiments_pearson.log - Logs of experiments run by 02.test_models_on_other_datasets_ensemble.ipynb notebook.
• LICENSE - Apache License 2.0
• Readme.MD - This file