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https://github.com/rdk/p2rank.git
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c6ee163ece
- Drop dead mask_unknown_residues=true from default(_rescore).groovy
(param removed from Params.groovy in 1b7809a6, 2019; configs missed)
- Rewrite distro/models/readme.md to match models on disk (add rescore_2024,
rescore_conservation; remove nonexistent conservation.model)
- Remove broken documentation/rescoring.md link from distro/README.md
- distro/config/readme.md: drop nonexistent working.groovy reference,
fix github link master->develop
- Delete dead commented-out method bodies in PdbUtils, RPlotter,
PredictionVisualizer
- Fix typo in Main.groovy javadoc
Directory with pre-trained models
Prank looks here for the model specified by the -model / -m parameter.
The model should always be used only in combination with the parameters or config file that was used to train it. I.e.: the feature extraction has to be executed with the same parameters.
List of models
P2Rank (pocket prediction)
default... configdefault.groovyconservation_hmm... configconservation_hmm.groovy(uses HMMER-based sequence conservation)alphafold... configalphafold.groovy(tuned for AlphaFold / NMR / cryo-EM structures, no b-factor)alphafold_conservation_hmm... configalphafold_conservation_hmm.groovy
PRANK (pocket rescoring)
default_rescore... configdefault_rescore.groovyrescore_2024... configrescore_2024.groovy(newer model, recommended for AlphaFold / NMR / cryo-EM)rescore_conservation... configrescore_conservation.groovy(rescoring with conservation features)
Auxiliary
_score_transform/— score-transformer JSON files (probability calibration, z-score) loaded by the models above.