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

Directories

• 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.
• ACDC_FOLDS - converted acdc-nn train folds from here and PROSTATA test results on Ssym and Ssym_r folds from here.

Notebooks

• 00.generate_datasets.ipynb - Process the DATA directory and generate the DATASETS directory.
• 01.add_megadataset_and_split_on_train_test_sets.ipynb Expand dataset with megadatasets data. Split on train and test sets. Generate PROSTATA_EXPERIMENTS directory.
• 02.test_models_by_folds.ipynb - Test each individual model in the ensemble using 5-fold cross validation
• 03.test_models_on_other_datasets_ensemble.ipynb - test the PROSTATA ensemble on various combinations of train and test datasets. test_*_with_predictions.csv containts tests set with prediction (pred_ddg) column.
• 04.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 a user sequence.

Other files

• environment.yml - conda environment.
• PROSTATA_experiments_pearson.log - Logs of experiments run by 03.test_models_on_other_datasets_ensemble.ipynb notebook.
• LICENSE - Apache License 2.0
• Readme.MD - This file