EViS

An Enhanced Virtual Screening Approach based on Pocket Ligand Similarity

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

About EViS

EViS is an enhanced virtual screening method which integrates ligand docking, protein pocket template searching and ligand template shape similarity calculating. A novel PL-score to characterize local pocket-ligand template similarity is used to evaluate the screening compounds. The docking poses (MOL2 format) obtained by any docking programs can be evaluated by PL-score comparing with the native pocket-ligand pairs in BioLip dataset.

Getting Started

Dependencies and Installing

• Before running EViS, the following packages should be installed.
• gcc: gcc-8.3.0
• python version : 2.7
• numpy: numpy 1.16.6
• git clone: https://github.com/JingHuangLab/EViS.git

Download and unzip the EViS package

• git clone https://github.com/JingHuangLab/EViS.git

• running the following commands

cd EViS 
tar -xvzf user_input.tar.gz 
module load gcc/gcc-8.3.0 

Executing program

EViS program needs two consecutive steps (please ensure the last step was completed before running the next step):

1, prepare the screening compounds (MOL2 format) and pocket ('.POC' format) into the input folder.

• put all compounds (MOL2 format) into (user_input/results_docking/ligand_mol2/) subfolder.

• put the pocket file (named as "nativepocket.poc") into the (user_input/results_docking/pocket/) subfolder.

  The pocket is like as:

POC     nativepocket
ATOM    253  N   VAL A  49       6.937   3.497 -28.457  1.00 34.68           N
ATOM    254  CA  VAL A  49       6.465   2.179 -28.887  1.00 34.68           C
ATOM    255  C   VAL A  49       5.665   2.297 -30.179  1.00 34.68           C
ATOM    256  O   VAL A  49       5.965   1.651 -31.192  1.00 34.68           O
...
TRE

If you are still not sure the input files, you can check the example files in this repository.

2, runEViS.py

For exmple：

cd script
python run_EViS.py

output:

pocket folder:

• pocket_align.POC : all pocket templates for nativepocket.poc with similarity >0.5
• pocket_topN.info : top 50 (maximum) template pockets information
• pocket_topN.mol2 : the template ligands binding with the topN template pockets in BioLip dataset.

ligands_mol2 folder:

• .lsalign ： the similarity file between the screening compound and topN template ligands save in "pocket_topN.mol2"

results_docking folder:

• PLscore.result : the final PL-score results for the screening compounds.

Help

If you have any questions, please contact with Wenyi Zhang(zhangwenyi@westlake.edu.cn)

Authors

• Wenyi Zhang (zhangwenyi@westlake.edu.cn)
• JingHuang (Huangjing@westlake.edu.cn)

Acknowledgments

Inspiration, code snippets, etc.

• LS-align
• PPS-align
• ITASSER