Astex PLI

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

DOI: 10.1021/acs.jmedchem.6b00716

We are actively developing the PLI code and will release an updated version in July 2016.

Features

• Score protein-ligand interactions (for example docking/VS poses)
• Solvent Mapping
• Generate Interaction Maps for Donor/Acceptor/Lipophile etc.
• Rich atom-typing

Installation

System Requirements

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

Download

• A zip of the current repository and tagged releases (as they become available) can be found at bitbucket.

Via Git

• 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

Installing

Once you have obtained the code (either by extracting a snapshot or cloning the repository:

• cd to the directory <dir>
• Type make in <dir>. This should compile the code and create a binary <dir>/bin/pli.
• Set the environment variable PLI_DIR to <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

Modes

To see a list of modes and command-line options run

$PLI_DIR/bin/pli -help

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"

Licence

Apache 2.0 License, see licence.txt for details.

Acknowledgements

• Brendan McConkey - for the capped and weighted Voronoi partitioning code (see the original publication)
• John Burkardt - whose SPHERE_LEBEDEV_RULE program was used to calculate lebedev points.
• The PDB - and the thousands of authors who have deposited X-ray structures of protein-ligand complexes.