DeepRank

DeepRank is a general, configurable deep learning framework for data mining protein-protein interactions (PPIs) using 3D convolutional neural networks (CNNs).

DeepRank contains useful APIs for pre-processing PPIs data, computing features and targets, as well as training and testing CNN models.

DeepRank highlights:

  • Predefined atom-level and residue-level PPI feature types
    • e.g. atomic density, vdw energy, residue contacts, PSSM, etc.
  • Predefined target types
    • e.g. binary class, CAPRI categories, DockQ, RMSD, FNAT, etc.
  • Flexible definition of both new features and targets
  • 3D grid feature mapping
  • Efficient data storage in HDF5 format
  • Support both classification and regression (based on PyTorch)