Protein-Ligand Interaction Analysis with PLIP

You can use PLIP to identify non-covalent interactions between biological macromolecules and their ligands easily, and there's a web server hosted, that you can use without any deployment.

Unfortunately, you can only submit one structure to the web server at a time. So if you have lots of structures to analyze, it's a good idea to run it locally. In my situation, running it with Docker is simple and meets needs.

pharmai/plip
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
Python464107

This note is based on macOS, you can take it as a reference if you run PLIP on Linux.

Detailed procedure#

Install docker:
1. macOS: download docker from the website and install it just like many other software and run it after installation.
2. Linux:
  
  If your server is in China, it is recommended to use Aliyun's image acceleration. The installation command is as follows:
```
curl -fsSL https://get.docker.com | bash -s docker --mirror Aliyun
```
  In other countries, you can directly use the official script to install:
```
curl -fsSL https://get.docker.com | bash -s docker
```
  If you successfully installed Docker and Docker-Compose, you can view the version with the following command:
```
docker -v
docker compose version
```
Make working directory
```
mkdir -p $HOME/PLIP/pdb
```
Put the pdb files that need analysis file in $HOME/PLIP/pdb.

Run FLIP

cd $HOME/PLIP/pdb

docker run --rm \
    -v ${PWD}:/results \
    -w /results \
    -u $(id -u ${USER}):$(id -g ${USER}) \
    pharmai/plip:latest -f $HOME/pdb/* -xtyp

Parameters：

-f The same can be done for local PDB files (-f <file>) or for reading from stdin (-f -).
-i PLIP can automatically fetch the entry from the PDB server when a valid PDB ID is provided.

XML report files (-x, best for automatic processing)
Text report files (-t, human-readable)
PyMOL session files (-y)
PyMOL Ray-traced images (-p)
writing to stdout (-O), to be used in combination with XML or text report files

此文由 Mix Space 同步更新至 xLog
原始链接为 https://xxu.do/posts/academic/Protein-Ligand-Interaction-Analysis-with-PLIP