PyPLIF is a program/script written in Python to analyze protein-ligand interaction from the molecular docking result. It relies on OpenBabel module to read and process the molecule files from the molecular docking output. The current version only support the Sybil mol2 format, but it is planned to support other format in the future release such as pdbqt and dlg from Autodock and Autodock Vina. Unfortunately the current version is specially designed for analyzing the docking results from PLANTS docking software.
Please use the following citations to acknowledge the use of PyPLIF in your works:
1. Radifar M, Yuniarti N, Istyastono EP. PyPLIF-assisted redocking indomethacin-(R)-alpha-ethyl-ethanolamide into cyclooxygenase-1. Indones. J. Chem. 2013, 13(3):283–286 | Click here to download the article in pdf.
2. Radifar M, Yuniarti N, Istyastono EP. PyPLIF: Python-based Protein-Ligand Interaction Fingerprinting. Bioinformation. 2013, 9(6):325-328 | doi: 10.6026/97320630009325 | PubMed PMID: 23559752 | Click here to download the article in pdf.
We started the project and put PyPLIF in the following link: https://code.google.com/archive/p/pyplif/. Since the maintenance of the site has been stopped, the project site has moved to https://github.com/radifar/pyplif. However, for your convenience we put also the latest stable version of PyPLIF (PyPLIF 0.1.1) in our own server. Click here to download the software.
Based on our experiences, PyPLIF works perfectly in Ubuntu 10.04 LTS and 12.04 LTS. Unfortunately, our experiences have also told us that PyPLIF could not longer work with newer Ubuntu version. Therefore, we suggest to stick with Ubuntu 10.04 LTS or 12.04 LTS to work with PyPLIF. Click here for more detail information on how to install and work with PyPLIF.