mirror of
https://github.com/rdk/p2rank.git
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913e0b551e
- Add SwinSite and Seq2Pocket rows to the supported methods table, with GitHub + paper links and a note that they point at per-protein directories rather than single files - Add a "Rescoring directory-based predictions" example covering the per-directory dataset pattern - Add a "Conservation-aware rescoring" section documenting -c rescore_conservation and the .hom file requirement - Quick Start: add a swinsite example line
215 lines
8.2 KiB
Markdown
215 lines
8.2 KiB
Markdown
# Rescoring Predictions from Other Methods
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P2Rank can rescore pocket predictions from other binding site prediction tools,
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re-ranking their pockets using its own ML model.
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## Quick Start
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```bash
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prank rescore test_data/fpocket.ds # rescore fpocket predictions
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prank rescore test_data/pocketeer.ds -o rescore_pocketeer # rescore pocketeer, output to specific dir
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prank eval-rescore test_data/fpocket.ds # rescore and evaluate against known ligands
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prank fpocket-rescore test_data/basic.ds # run fpocket and rescore in one step
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prank rescore test_data/pocketeer.ds -c rescore_2024 # use new experimental rescoring model
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```
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## Commands
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| Command | Description |
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|---------|--------------------------------------------------------------------------------------------------------------------------------|
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| `prank rescore <dataset.ds>` | Rescore predictions and output re-ranked pockets. |
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| `prank eval-rescore <dataset.ds>` | Rescore and evaluate against known ligands. |
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| `prank fpocket-rescore <dataset.ds>` | Run Fpocket on proteins, then rescore.<br> Convenience shortcut that can be used as a drop-in replacement for `prank predict`. |
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## Supported Methods
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| Method | `PREDICTION_METHOD` | Prediction column points to | Links |
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|--------|--------------------|-----------------------------|-------|
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| Fpocket | `fpocket` | Fpocket output file (`.pdb`/`.cif`) | [GitHub](https://github.com/Discngine/fpocket), [paper](https://doi.org/10.1186/1471-2105-10-168) |
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| Pocketeer | `pocketeer` | `pockets.json` file | [GitHub](https://github.com/cch1999/pocketeer) |
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| PUResNetV2.0 | `puresnet` | Directory with `*.pkt.pdb` files | [GitHub](https://github.com/jivankandel/PUResNetV2.0), [paper](https://doi.org/10.1186/s13321-024-00865-6) |
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| ConCavity | `concavity` | `*_pocket.pdb` grid file | [project page](https://compbio.cs.princeton.edu/concavity/), [paper](https://doi.org/10.1371/journal.pcbi.1000585) |
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| SiteHound | `sitehound` | `*_summary.dat` file | [paper](https://pmc.ncbi.nlm.nih.gov/articles/PMC2703923/) |
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| DeepSite | `deepsite` | Results PDB file | [paper](https://doi.org/10.1093/bioinformatics/btx350) |
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| MetaPocket2 | `metapocket2` | PDB file with MPT residues | [paper](https://academic.oup.com/bioinformatics/article/27/15/2083/402380) |
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| LISE | `lise` | PDB file with HETATM records | [paper](https://academic.oup.com/nar/article/41/W1/W292/1094035) |
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| P2Rank | `p2rank` | `*_predictions.csv` file | [GitHub](https://github.com/rdk/p2rank), [paper](https://doi.org/10.1186/s13321-018-0285-8) |
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| SwinSite | `swinsite` | Per-protein directory with `grid<N>_score_<S>.mol2` files | [GitHub](https://github.com/ding-oh/SwinSite), [paper](https://doi.org/10.1021/acs.jcim.5c02734) |
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| Seq2Pocket | `seq2pocket` | Per-protein directory with `<ID>_predictions.txt` | [GitHub](https://github.com/skrhakv/seq2pocket), [paper](https://doi.org/10.64898/2026.01.28.702257) |
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The last two methods point the `prediction` column at a **per-protein directory**
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rather than a single file. See [Rescoring directory-based predictions](#rescoring-directory-based-predictions-swinsite-seq2pocket)
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below for an example.
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## Dataset File Format
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A dataset file (`.ds`) tells P2Rank which prediction method was used, and lists
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pairs of prediction output files and their corresponding protein structures.
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```text
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# Lines starting with # are comments
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PARAM.PREDICTION_METHOD=<method>
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HEADER: prediction protein
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path/to/prediction_output path/to/protein.pdb
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```
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**Required elements:**
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- `PARAM.PREDICTION_METHOD` -- name of the prediction method (see table above)
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- `HEADER:` line -- defines column order (must include `prediction` and `protein`)
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- Data rows -- whitespace-separated paths (relative to the `.ds` file location)
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The `protein` column should point to the structure that was used as input to the
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prediction tool. For `eval-rescore`, the protein must contain ligands (to compute
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evaluation metrics). For plain `rescore`, ligands are not needed.
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The column order in `HEADER:` is flexible -- `prediction protein` or
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`protein prediction` are both valid.
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## Examples
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### Rescoring Fpocket predictions
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`my_fpocket.ds`:
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```text
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PARAM.PREDICTION_METHOD=fpocket
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HEADER: prediction protein
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fpocket_output/1abc_out/1abc_out.pdb structures/1abc.pdb
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fpocket_output/2xyz_out/2xyz_out.pdb structures/2xyz.pdb
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```
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```bash
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prank rescore my_fpocket.ds
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```
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### Rescoring Pocketeer predictions
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`my_pocketeer.ds`:
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```text
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PARAM.PREDICTION_METHOD=pocketeer
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HEADER: prediction protein
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pocketeer_output/1abc/pockets.json structures/1abc.pdb
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pocketeer_output/2xyz/pockets.json structures/2xyz.cif
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```
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```bash
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prank rescore my_pocketeer.ds
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```
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### Evaluating rescoring quality
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Use `eval-rescore` with liganated proteins to compare the original ranking
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against the rescored ranking. This works with any supported method.
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`my_eval.ds`:
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```text
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PARAM.PREDICTION_METHOD=fpocket
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HEADER: prediction protein
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fpocket_output/1abc_out/1abc_out.pdb liganated/1abc.pdb
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fpocket_output/2xyz_out/2xyz_out.pdb liganated/2xyz.pdb
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```
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```bash
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prank eval-rescore my_eval.ds
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```
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This outputs evaluation metrics (DCA, DSO success rates, etc.) showing whether
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rescoring improved pocket ranking.
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### Rescoring directory-based predictions (SwinSite, Seq2Pocket)
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For these methods, the `prediction` column points to the per-protein output
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directory (not a single file). The loader picks up the expected files inside:
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`grid*_score_*.mol2` for SwinSite, `<ID>_predictions.txt` for Seq2Pocket.
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`my_swinsite.ds`:
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```text
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PARAM.PREDICTION_METHOD=swinsite
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HEADER: prediction protein
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swinsite_output/1abc structures/1abc.pdb
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swinsite_output/2xyz structures/2xyz.pdb
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```
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```bash
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prank rescore my_swinsite.ds
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```
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The same pattern applies to `seq2pocket`: point each row at the directory
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containing its `_predictions.txt`.
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## Output
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For each protein, two files are generated in the output directory:
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| File | Contents |
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|------|----------|
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| `{name}_rescored.csv` | Re-ranked pockets with new scores |
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| `{name}_predictions.csv` | Pocket details (scores, centers, residues, surface atoms) |
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The `_rescored.csv` contains columns:
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| Column | Description |
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|--------|-------------|
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| `name` | Pocket name |
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| `score` | New score assigned by P2Rank |
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| `rank` | New rank (after rescoring) |
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| `old_rank` | Original rank from the prediction method |
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PyMOL visualization files are also generated by default (disable with `-visualizations 0`).
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## Parameters
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Override parameters on the command line with `-param value`.
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A few commonly used parameters:
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```bash
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prank rescore dataset.ds -o output_dir -threads 4 -visualizations 0
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```
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| Parameter | Default | Description |
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|-----------|---------|-------------|
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| `-o` | auto-generated | Explicit output directory (overrides default) |
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| `-threads` | all CPUs | Number of parallel threads |
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| `-visualizations` | `true` | Generate PyMOL visualization files |
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| `-fail_fast` | `false` | Stop on first error |
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| `-model` | `default_rescore` | ML model to use for rescoring |
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## Experimental Rescoring Model (`rescore_2024`)
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An alternative rescoring model is available via `-c rescore_2024`. It uses a different feature set
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that does not depend on B-factor, making it suitable for AlphaFold models, NMR, and cryo-EM structures.
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```bash
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prank rescore fpocket.ds -c rescore_2024
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prank fpocket-rescore test.ds -c rescore_2024
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prank eval-rescore fpocket.ds -c rescore_2024
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```
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This model shows promising results but has not been fully evaluated yet.
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## Conservation-aware rescoring (`rescore_conservation`)
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A rescoring model that incorporates per-residue sequence conservation scores
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alongside the standard P2Rank features. Works with any supported prediction
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method, not just Fpocket.
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```bash
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prank rescore fpocket.ds -c rescore_conservation \
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-conservation_dirs path/to/cons/
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```
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Requires HMMER-based `.hom` conservation files (one per chain, named
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`{baseName}_{chainId}.hom`). See [conservation.md](conservation.md) for the
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file format and pipeline.
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