This directory contains documentation and tutorials for P2Rank.
Important
Start here: the User Guide is a comprehensive introduction covering installation, prediction, rescoring, configuration, performance tuning, and more.
| File | Description |
|---|---|
| rescoring.md | Rescoring predictions from other pocket prediction methods (Fpocket, Pocketeer, etc.) |
| docking.md | Deriving docking search boxes (center + size) from predicted pockets |
| export-points.md | Exporting SAS points with feature vectors and predicted ligandability scores |
| export-pocket-grid.md | Exporting per-pocket 3D grid points (PyMOL/ChimeraX-ready) |
| export-pocket-descriptors.md | Exporting per-pocket scalar descriptors (volume, sphericity, principal moments, ...) |
| cofactors.md | Treating selected HETATM groups as part of the protein surface |
| aa-mapping.md | Non-canonical amino acid residue mapping to standard residues |
| conservation.md | Conservation-aware prediction (HMM-based) |
| utility-commands.md | Reference for analyze, transform, and print subcommands |
| File | Description |
|---|---|
| training-tutorial.md | Training and evaluating custom models, crossvalidation, grid optimization |
| feature-setup.md | Feature vector configuration and introduction to adding new features |
| new-feature-evaluation-tutorial.md | Implementing a new feature and evaluating its contribution to prediction |
| hyperparameter-optimization-tutorial.md | Grid and Bayesian optimization of algorithm parameters |
| training-score-transformers.md | Training probability and z-score transformers for pocket and residue scores |