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)