p2rank
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rdk
P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
https://github.com/rdk/p2rank/issues/59 Stop logging to distribution directory -- instead log to stderr to stderr.
In https://github.com/rdk/p2rank/blob/develop/distro/prank the program logs to a logfile, that is default inside the installation directory. I believe this is the run-script distributed in the release tarball. When installing this on...
Hi, It seems the file name in `*.ds` file does not support an absolute path like `/home/user/dataset/*.pdb`. I have a `.ds` file: ``` /home/jsun/gpse_v2/test/structure_dataset/A0A1Q8LK65_AF.pdb /home/jsun/gpse_v2/test/structure_dataset/W7ISS8_AF.pdb /home/jsun/gpse_v2/test/structure_dataset/A5EDZ7_AF.pdb /home/jsun/gpse_v2/test/structure_dataset/A0A3G7HEQ2_AF.pdb /home/jsun/gpse_v2/test/structure_dataset/A0A6J4VWF3_AF.pdb /home/jsun/gpse_v2/test/structure_dataset/A0A1R4K1N1_AF.pdb /home/jsun/gpse_v2/test/structure_dataset/A0A7W8E001_AF.pdb...
Just came across P2Rank and interested to run it on a zipped folder containing protein conformations from a trajectory. I have pymol installed on the linux cluster and I did...
I run these commands, where joined.ds is from: https://github.com/rdk/p2rank-datasets ./prank.sh analyze residues joined.ds ./prank analyze fasta-masked joined.ds But several files with residues don`t match with the fasta sequence. All the...
I was trying to train a new model on train dataset (holo4k_train.ds containing 3634 proteins) and validation dataset (holo4k_test.ds containing 409 proteins) (memory settings: $JAVA_OPTS -Xmx16G) using the following command:...
If a structure (for example 1tqn) is fetched in PyMOL, exported to mmCIF and then imported to P2Rank then it seems to be failing.
Is there an easy way to access the feature descriptor of the SAS points?
This documentation can be later used to create automated release using GitHub actions.
