Skip to content

Commit

Permalink
update readme
Browse files Browse the repository at this point in the history
  • Loading branch information
rdk committed Nov 7, 2024
1 parent 3eaa6c7 commit bc9b02d
Showing 1 changed file with 5 additions and 6 deletions.
11 changes: 5 additions & 6 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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.

Expand All @@ -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
Expand All @@ -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**
Expand Down

0 comments on commit bc9b02d

Please sign in to comment.