From bc6be77f81de316ebe6c119429f054a334b2f5f1 Mon Sep 17 00:00:00 2001 From: rdk Date: Sat, 29 Jun 2024 10:44:38 +0200 Subject: [PATCH] update readme --- README.md | 37 +++++++++++++++++++++++++------------ 1 file changed, 25 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 84496592..a61e441d 100644 --- a/README.md +++ b/README.md @@ -15,8 +15,11 @@ Ligand-binding site prediction based on machine learning. ### Description P2Rank is a stand-alone command line program that predicts ligand-binding pockets from a protein structure. It achieves high prediction success rates without relying on an external software for computation of complex features or on a database of known protein-ligand templates. - -Version 2.4 adds support for `.cif` input and contains a special profile for predictions on AlphaFold models and NMR/cryo-EM structures. + +### What's new? + +* Version 2.4.2 adds support for BinaryCIF (`.bcif`) input and rescoring of fpocket predictions in `.cif` format. +* Version 2.4 adds support for mmCIF (`.cif`) input and contains a special profile for predictions on AlphaFold models and NMR/cryo-EM structures. ### Requirements @@ -24,7 +27,6 @@ Version 2.4 adds support for `.cif` input and contains a special profile for pre * PyMOL 1.7 (or newer) for viewing visualizations (optional) P2Rank is tested on Linux, macOS, and Windows. -On Windows, it is recommended to use the `bash` console to execute the program instead of `cmd` or `PowerShell`. ### Setup @@ -83,8 +85,10 @@ prank help prank predict test.ds # run on dataset containing a list of pdb/cif files prank predict -f test_data/1fbl.pdb # run on a single pdb file -prank predict -f test_data/1fbl.cif # run on a single cif file -prank predict -f test_data/1fbl.pdb.gz # run on a single gzipped pdb file +prank predict -f test_data/1fbl.cif # run on a single mmCIF file +prank predict -f test_data/1fbl.bcif # run on a single BinaryCIF file +prank predict -f test_data/1fbl.pdb.gz # run on a single gzipped pdb file (other formats can be compressed too) +prank predict -f test_data/1fbl.cif.zst # run on a single cif file compressed with Zstandard prank predict -threads 8 test.ds # specify num. of working threads for parallel dataset processing prank predict -o output_here test.ds # explicitly specify output directory @@ -109,7 +113,7 @@ prank predict -c alphafold test.ds # use alphafold config and model (confi ### Configuration -You can override the default params with a custom config file: +You can override the default parameters values in a custom config file: ~~~bash prank predict -c config/example.groovy test.ds @@ -117,7 +121,7 @@ prank predict -c example test.ds # same effect, config/ is defaul ~~~ -It is also possible to override the default params on the command line using their full name. +It is also possible to override parameters on the command line using their full name after `-` (not `--`). ~~~bash prank predict -visualizations 0 -threads 8 test.ds # turn off visualizations and set the number of threads @@ -125,9 +129,9 @@ prank predict -c example.groovy -visualizations 0 -threads 8 test.ds # overr ~~~ P2Rank has numerous configurable parameters. -To see the list of standard params look into `config/default.groovy` and other example config files in this directory. -To see the complete commented list of all (including undocumented) -params see [Params.groovy](https://github.com/rdk/p2rank/blob/develop/src/main/groovy/cz/siret/prank/program/params/Params.groovy) in the source code. +To see the list of standard parameters look into `config/default.groovy` and other example config files in this directory. +To see the complete commented list of all (including undocumented) +parameters see [Params.groovy](https://github.com/rdk/p2rank/blob/develop/src/main/groovy/cz/siret/prank/program/params/Params.groovy) in the source code. ### Evaluate prediction model @@ -142,7 +146,14 @@ prank eval-predict test.ds In addition to predicting new ligand binding sites, P2Rank is also able to rescore pockets predicted by other methods -(Fpocket, ConCavity, SiteHound, MetaPocket2, LISE and DeepSite are supported at the moment). +(Fpocket, +ConCavity, +SiteHound, +MetaPocket2, +LISE, +DeepSite, +and PUResNetV2.0 +are supported at the moment). ~~~bash prank rescore test_data/fpocket.ds @@ -150,6 +161,8 @@ prank rescore fpocket.ds # test_data/ is default 'dataset_base_d prank rescore fpocket.ds -o output_dir # test_output/ is default 'output_base_dir' prank eval-rescore fpocket.ds # evaluate rescoring model ~~~ + +Note: for rescoring the dataset file needs to have a specific 2-column format. See examples in `test_data/fpocket.ds`. ## Build from sources @@ -168,7 +181,7 @@ Now you can run the program via: distro/prank # standard mode that is run in production ./prank.sh # development/training mode ``` -To use `./prank.sh` (development/training mode) first you need to copy and edit `misc/locval-env.sh` into repo root directory (see https://github.com/rdk/p2rank/blob/develop/misc/tutorials/training-tutorial.md#preparing-the-environment). +To use `./prank.sh` (development/training mode) first you need to copy and edit `misc/locval-env.sh` into repo root directory (see [training tutorial](https://github.com/rdk/p2rank/blob/develop/misc/tutorials/training-tutorial.md#preparing-the-environment)). ## Comparison with Fpocket