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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 & dlg from Autodock and Autodock Vina. Unfortunately the current version is specially designed for analyzing the docking results from PLANTS <http://www.tcd.uni-konstanz.de/research/plants.php> If you use this program for your work please include the following reference: Radifar, M., 2012, PyPLIF version 0.1 beta, http://code.google.com/p/pyplif/ (accessed date). Replace date with the date when you download this program. Installation ------------ The instruction here is for installing PyPLIF as a module, for installing PyPLIF as the stand-alone program check INSTALL.txt To install PyPLIF module just use this command: sudo python setup.py install Getting Started --------------- Requirements: * To use this program you should use the output from PLANTS. * The ligand's conformation should be separated, that's the write_multi_mol2 should be disabled by putting this line into the PLANTS configuration file: write_multi_mol2 0 Here's how to use PyPLIF step by step: * Makes sure PyPLIF already installed, check INSTALL.txt for the complete instruction * Prepare the PyPLIF input by docking any ligand and protein you want * Prepare config file for PyPLIF, the name can be anything but by default PyPLIF will looking for 'config.txt', the config file example can be found in docs folder. The content of it should be self-explaining. * Also prepare the reference ligand and the reference protein conformation in mol2 format. * Run pyplif simply by entering the command 'pyplif'. * After pyplif finished the calculation the output file will appear showing the molecule file name, score, interaction bit, and Tc-IFP (Tanimoto coefficient Interaction Fingerprinting) Tips: It is highly suggested to use the protein binding site instead of the whole protein since using the binding site is much faster than using the whole protein. You can use PLANTS to produce the binding site using the following command: PLANTS --mode bind molecule.mol2 x protein.mol2 where the 'molecule.mol2' is the ligand file, x is the additional distance from the ligand sphere, where the ligand sphere's radius is from the ligand center to the outermost ligand atom. That command will produce PLANTSactiveSite.mol2 and PLANTSactiveSiteResidues.mol2, you can use the latter as the binding site input for PyPLIF. Tutorial -------- Before you start makes sure that SPORES (http://www.tcd.uni-konstanz.de/research/spores.php) is already installed in your computer. This tutorial is based on the paper 'Crystal Structure-Based Virtual Screening for Fragment-like Ligands of the Human Histamine H1 Receptor' (http://pubs.acs.org/doi/abs/10.1021/jm2011589) The ligands used in this tutorial is taken from the SMILES from the supplementary information of that paper. First go to docs/ligands folder and run smitomol2.sh: ./smitomol2.sh That script will convert the active ligands (CNS_actives_less.smi) and decoys (Decoys_less.smi) for HRH1 (Histamine Receptor H1) to mol2 format. The final result will be H1_ligands_ready.mol2 which will be used for retrospective validation of PLANTS against HRH1 receptor. Next go to docs folder and run PLANTS by entering this command: PLANTS --mode screen plants.conf After the docking is finished you can run pyplif by entering this command: pyplif OR pyplif -c config.txt -o ifpresult.csv The '-c' or '--config' option is for choosing the configuration file aside from the default one (which is config.txt). While the '-o' or '--output' is for choosing the output file, if output file has been stated in configuration file then the '-o' option will overwrite that option.