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.
Much of the PLI methodology was published recently:
Protein-Ligand-Informatics force field (PLIff): towards a fully knowledge driven “force field” for biomolecular interactions
M.L. Verdonk, R.F. Ludlow, I. Giangreco, and P.C. Rathi
J. Med. Chem., Just Accepted Manuscript
We are actively developing the PLI code and will release an updated version in July 2016.
- Score protein-ligand interactions (for example docking/VS poses)
- Solvent Mapping
- 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.