Subcellular-Localization

Experiments on deep learning based subcellular localization of proteins using structural information

Folders

• data
  • Data.csv
  • deeploc_af2_df.xlsx
    • Excel sheet with all sequences and labels for training and testing
  • esm_feats.npy
• utils

Scripts

• run_esm.ipynb
  • train ESM2 on sequences of length 500
• evaluate_esm.ipynb
  • Evalutae ESM2 and other trained models
• train_cnn.ipynb
  • Train 3D AlexNet and VGG16 on voxellized proteins
• run_fusion.ipynb
  • Train mid level fusion model with ESM2 and 3D AlexNet/VGG16
• voxel_models.py
  • Contains classes for 3D models
• midfusion_mlp_cnn.py
• mlp_esm..ipynb
• pure_cnn.py