Protein-Ligand Interaction Analysis with PLIP

PLIP makes it easy to identify non-covalent interactions between biological macromolecules and their ligands. There's also a hosted web server 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 case, running it with Docker is simple and meets my needs.

https://github.com/pharmai/plip

This guide was written on macOS, but you can use it as a reference if you run PLIP on Linux.

Detailed procedure

Install Docker:
1. macOS: download Docker from the website, install it like any other software, and run it after installation.
2. Linux:
  If your server is in China, it's recommended to use Aliyun's image acceleration. The installation command is:
  BASH
  curl -fsSL https://get.docker.com | bash -s docker --mirror Aliyun
  Elsewhere, you can install it directly with the official script:
  BASH
  curl -fsSL https://get.docker.com | bash -s docker
  Once Docker and Docker Compose are installed, you can check their versions with the following commands:
  BASH
  docker -v docker compose version
Create a working directory
BASH
```
mkdir -p $HOME/PLIP/pdb
```
Put the PDB files you want to analyze into $HOME/PLIP/pdb.

Run PLIP

BASH

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   Takes a local PDB file (-f <file>) or reads from standard input (-f -).
-i   When a valid PDB ID is provided, PLIP can automatically fetch the entry from the PDB server.

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)