P2RANK

Ligand-binding site prediction.

Requirements

• Java 1.8 or newer for execution
• PyMOL 1.7.x for viewing visualizations

Example commands (can be executed here in the installation directory)

Print help:

prank help

Ligand binding site prediction (P2RANK algorithm):

prank predict test.ds # run on whole dataset (list of pdb files) prank predict -f test_data/liganated/1aaxa.pdb # run on individual pdb file prank predict test.ds -o output_here # explicitly specify output directory

prank predict -threads 8 test.ds # specify no. of working threads for parallel processing prank predict -c predict2.groovy test.ds # specify configuration file (predict2.groovy uses different prediction model and combination of parameters)

Evaluate model for pocket prediction:

prank eval-predict test.ds prank eval-predict -f test_data/liganated/1aaxa.pdb

Prediction output notes:

For each file in the dataset program produces a CSV file in the output directory named

<pdb_file_name>_predictions.csv, which contains an ordered list of predicted pockets, their scores, coordinates

of their centroids and list of PDBSerials of adjacent amino acids and solvent exposed atoms.

If coordinates connolly points that belong to individual pockets are needed they can be found

in viualisations/data/<pdb_file_name>_points.pdb. There "Residue sequence number" (23-26) of HETATM record

cocrresponds to the rank of corresponding pocket (points with value 0 do not belong to any pocket).

Rescore pocket detected by other methods (PRANK algorithm):

prank rescore test_data/fpocket.ds prank rescore fpocket.ds # test_data/ is default 'dataset_base_dir' prank rescore fpocket.ds -o output_dir # test_output/ is default 'output_base_dir'

Override default params with custom config file:

prank rescore -c config/example.groovy test_data/fpocket.ds prank rescore -c example.groovy fpocket.ds

It is also possible to override default params on a command line with their full name:

(to see complete list of params look into config/default.groovy)

prank rescore -seed 151 -threads 8 test_data/fpocket.ds prank rescore -c example.groovy -seed 151 -threads 8 test_data/fpocket.ds

Evaluate model for pocket rescoring:

prank eval-rescore fpocket-pairs.ds prank eval-rescore -m model/default.model fpocket-pairs.ds prank eval-rescore -m default.model fpocket-pairs.ds prank eval-rescore -m other.model fpocket-pairs.ds prank eval-rescore -m other.model fpocket-pairs.ds -o output_dir