diff --git a/README.md b/README.md index 535bfad7..695c57e6 100644 --- a/README.md +++ b/README.md @@ -121,7 +121,7 @@ prank predict -c alphafold test.ds # use alphafold config and model (confi ### Configuration -You can override the default parameters values in a custom config file: +You can override the default parameter values in a custom config file: ~~~bash prank predict -c config/example.groovy test.ds @@ -192,7 +192,7 @@ prank fpocket-rescore test.ds -fpocket_command "/bin/fpocket -w m" # specify cu prank fpocket-rescore test.ds -fpocket_keep_output 0 # delete fpocket output files ~~~ -In this case, the dataset file can be a simple list of pdb/cif files since Fpocket predictions will pe calculated ad-hoc. +In this case, the dataset file can be a simple list of pdb/cif files since Fpocket predictions will be calculated ad-hoc. `prank fpocket-rescore` will produce `predictions.csv` as well, so it can be used as an in-place replacement for `prank predict` in most scenarios. Note: if you use `fpocket-rescore`, please cite Fpocket as well. @@ -201,7 +201,7 @@ Note: if you use `fpocket-rescore`, please cite Fpocket as well. ## Build from sources This project uses [Gradle](https://gradle.org/) build system via included Gradle wrapper. -On Windows use `bash` to execute build commands (`bash` is installed as a part of [Git for Windows](https://git-scm.com/download/win)). +On Windows, use `bash` to run build commands (installed by default with [Git for Windows](https://git-scm.com/download/win)). ```bash git clone https://github.com/rdk/p2rank.git && cd p2rank @@ -220,15 +220,14 @@ To use `./prank.sh` (development/training mode) first you need to copy and edit ## Comparison with Fpocket [Fpocket](https://github.com/Discngine/fpocket) is a widely used open source ligand binding site prediction program. -It is fast, easy to use and well documented. As such, it was a great inspiration for this project. -Fpocket is written in C, and it is based on a different geometric algorithm. +It is fast, easy to use and well documented. As such, it served as a great inspiration for this project. Some practical differences: * **Fpocket** - has a much smaller memory footprint - runs faster when executed on a single protein - - produces a high number of less relevant pockets (and since the default scoring function isn't very effective the most relevant pockets often don't get to the top) + - produces a high number of less relevant pockets (and since the default scoring function isn't very effective, the most relevant pockets often don't get to the top) - contains MDpocket algorithm for pocket predictions from molecular trajectories - still better documented * **P2Rank**