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.

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

Detailed procedure

1. 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

2. Make working directory

   mkdir -p $HOME/PLIP/pdb

3. Put the pdb files that need analysis file in $HOME/PLIP/pdb.

4. 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