DeepRank2 2.1.1 documentation
DeepRank2 is an open-source deep learning (DL) framework for data mining of protein-protein interfaces (PPIs) or single-residue variants (SRVs). This package is an improved and unified version of three previously developed packages: DeepRank, DeepRank-GNN, and DeepRank-Mut.
DeepRank2 allows for transformation of (pdb formatted) molecular data into 3D representations (either grids or graphs) containing structural and physico-chemical information, which can be used for training neural networks. DeepRank2 also offers a pre-implemented training pipeline, using either convolutional neural networks (for grids) or graph neural networks (for graphs), as well as output exporters for evaluating performances.
Predefined atom-level and residue-level feature types (e.g. atom/residue type, charge, size, potential energy, all features’ documentation is available under Features notes)
Predefined target types (binary class, CAPRI categories, DockQ, RMSD, and FNAT, detailed docking scores documentation is available under Docking scores notes)
Flexible definition of both new features and targets
Features generation for both graphs and grids
Efficient data storage in HDF5 format
This section documents the DeepRank2 API.