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protein-vae's Introduction

Explore protein conformational space with variational autoencoder

Python 3.6+ Apache license Paper DOI

File explanation

Main

  1. align_trajs.py: align trajectories
  2. maps_featurize.py: turn traj data into xyz features
  3. training.py: train VAE/AE models
  4. models.py: model architecture for encoder, decoder and VAE

Utils

  1. PDB_process.py: extract PDB template and write new coordinates
  2. DOPE.py: calculate DOPE score of the given PDB
  3. evaluation.py: evaluate the performance of VAE/AE models

Dependencies

The dependencies are listed in requirements.txt file.

For DOPE score calculation, modeller is required and can be downloaded here.

License

Apache-2.0

protein-vae's People

Contributors

hhaootian avatar

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