PLI is a program developed at Astex Pharmaceuticals for scoring protein-ligand interactions. Interacting atoms are defined using a modified Voronoi partitioning and interaction propensities (including geometric preferences) have been derived from over 30,000 PDB entries.
- Score protein-ligand interactions (for example docking/VS poses)
- Fragment mapping (PLImap) as described here
- Generate Interaction Maps for Donor/Acceptor/Lipophile etc.
- Rich atom-typing
PLI is written in C and has been developed and tested on 64-bit Linux (CentOS) using the gcc compiler. It has no major external dependencies.
Obtaining the Code
- A zip of the current repository and tagged releases (as they become available) can be found at bitbucket.
- You can fork the repository on bitbucket (you will need an account) or clone the repository from the command line
git clone https://bitbucket.org/AstexUK/pli.git
Once you have obtained the code (either by extracting a snapshot or cloning the repository:
cdto the directory
<dir>. This should compile the code and create a binary
- Set the environment variable
<dir>, e.g. for bash:
PLI_DIR=/path/to/pli export PLI_DIR
- Try running one of the examples in the examples directory, e.g:
cd $PLI_DIR/examples $PLI_DIR/bin/pli -settings $PLI_DIR/examples/1a9u_contacts.pli
To see a list of modes and command-line options run
Get In Touch
If you have questions about PLI or have found it useful, let us know, on bitbucket or by email: "pli-at-astx-dot-com"
Apache 2.0 License, see licence.txt for details.