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Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al. (2025), https://doi.org/10.1093/nar/gkaf361
| Date | Stars |
|---|---|
| 2026-07-24 | 704 |
| 2026-07-25 | 704 |
| 2026-07-28 | 704 |
| 2026-07-30 | 704 |
| 2026-08-06 | 704 |
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# Protein-Ligand Interaction Profiler (PLIP)
Analyze noncovalent protein-ligand interactions in 3D structures with ease.
<img src="pliplogo.png" alt="PLIP Logo" height="100">
| Use Case | [Web Server](https://plip-tool.biotec.tu-dresden.de) | Docker | Singularity | Python Module | [Colab](https://colab.research.google.com/drive/1KV0Yx6vMFXvtyIRtmkPoMLN0Q6GKG1pm?usp=sharing) |
|---------------------------------------------------------------------------|--------------------|--------------------|--------------------|--------------------|--------------------|
| "I want to analyze my protein-ligand complex!" | :heavy_check_mark: | :heavy_check_mark: | :yellow_circle: | :x: | :heavy_check_mark: |
| "I want to analyze *a billion* protein-ligand complexes!" | :x: | :yellow_circle: | :heavy_check_mark: | :yellow_circle: | :x: |
| "I love the Linux command line and want to build a workflow around PLIP!" | :x: | :heavy_check_mark: | :heavy_check_mark: | :yellow_circle: |:x: |
| "I'm a Python programmer and want to use PLIP in my project!" | :x: | :yellow_circle: | :yellow_circle: | :heavy_check_mark: | :yellow_circle: |
| "I want to analyze large complexes!" | :x: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: |
---
## Quickstart
### Docker
If you have Docker installed, you can run a PLIP analysis for the structure `1vsn` with the following shell command:
On Linux / MacOS:
```bash
$ docker run --rm \
-v ${PWD}:/results \
-w /results \
-u $(id -u ${USER}):$(id -g ${USER}) \
pharmai/plip:latest -i 1vsn -yv
```
On Windows:
```bash
$ docker run --rm \
-v ${PWD}:/results \
-w /results \
-u $(id -u ${USER}):$(id -g ${USER}) \
pharmai/plip:latest -i 1vsn -yv
```
### Singularity
The equivalent command for our pre-built [Singularity](https://singularity.lbl.gov/) image for Linux (available under [Releases](https://github.com/pharmai/plip/releases)) is as follows:
```bash
$ ./plip.simg -i 1vsn -yv
```
Singularity allows to use PLIP with ease in HPC environments. Note that you need to have Singularity installed on your base system.
### Google Colab
PLIP is available as a [Google Colab](https://colab.research.google.com/drive/1KV0Yx6vMFXvtyIRtmkPoMLN0Q6GKG1pm?usp=sharing) to be used without the need to install it locally. It can be used without constraints in terms of
PDB file and protein sizes.
---
## Usage
This README provides instructions for setup and using basic functions of PLIP.
For more details, see the [Documentation](DOCUMENTATION.md).
### 1. Install PLIP
#### Containerized Image (recommended)
:exclamation: We ship PLIP as pre-built containers for multiple architectures (amd64/ARM), available on the [Docker Hub](https://hub.docker.com/r/pharmai/plip) or as pre-built Singularity image under [Releases](https://github.com/pharmai/plip/releases). See the quickstart section above for usage instructions.
#### Dependencies
If you cannot use the containerized bundle or want to use PLIP sources, make sure you have the following requirements installed:
- Python >= 3.6.9
- [OpenBabel](#Installing-OpenBabel) >= 3.0.0 with [Python bindings](https://open-babel.readthedocs.io/en/latest/UseTheLibrary/PythonInstall.html)
- PyMOL >=Excerpt of 12,309 characters
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Would you bet a product on this? Bounded 0–100 and slow moving.
matched fp:d9fe08399192455b, topic:bioinformatics, topic:scientific-computing, desc:protein