danqingmk / l-score

L-Score

The rescoring module uses pocket similarity search algorithm PPS-align to obtain the top 50 template pockets with similarity score, and the compound library was then rescored using the ligand similarity comparison algorithm LS-align with the corresponding cocrystal ligand as the template ligands.

Installation

Rescoring module is built on Python3, we recommend using Anaconda environment as enviroment management. The virtual environment can be created as follows:

conda create -n your_environment python==3.7
conda activate your_environment

Download the source code of rescore from GitHub:

git clone https://github.com/danqingmk/L-Score.git

Executing program

Rescoring module needs two steps before running the program:

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 "4AF3.poc") into the (user_input/results_docking/pocket/) subfolder. The pocket is like as:

POC     4AF3
ATOM      1  N   LEU A  83      22.048 -28.324 -12.736  1.00 66.94           N  
ATOM      2  CA  LEU A  83      22.513 -26.988 -12.326  1.00 67.60           C  
ATOM      3  C   LEU A  83      23.247 -26.970 -10.976  1.00 68.95           C  
ATOM      4  O   LEU A  83      24.299 -26.348 -10.841  1.00 71.15           O  
ATOM      5  CB  LEU A  83      21.340 -25.998 -12.295  1.00 65.27           C  
ATOM      6  CG  LEU A  83      20.742 -25.539 -13.638  1.00 65.01           C  
ATOM      7  CD1 LEU A  83      19.453 -24.785 -13.366  1.00 63.47           C  
ATOM      8  CD2 LEU A  83      21.694 -24.676 -14.465  1.00 62.76           C  
ATOM      9  N   GLY A  84      22.709 -27.656  -9.980  1.00 70.39           N  
ATOM     10  CA  GLY A  84      23.266 -27.567  -8.627  1.00 73.87           C  
ATOM     11  C   GLY A  84      24.722 -27.969  -8.445  1.00 74.98           C  
...
TRE

2. run_LS.py

python run_LS.py

Examples of results

Ranking	    Compound ID	        Rescore
1	active_CHEMBL4100838	0.8648
2	active_CHEMBL4068526	0.8633
3	active_CHEMBL2023494	0.854
4	active_CHEMBL4074076	0.85
5	active_CHEMBL1171837	0.8492
6	active_CHEMBL4059858	0.8461
7	active_CHEMBL4847875	0.844
8	active_CHEMBL4063659	0.8425
9	active_CHEMBL5197530	0.842
10	active_CHEMBL3646210	0.8396
11	active_CHEMBL4085366	0.8396
12	active_CHEMBL5186979	0.8373
13	active_CHEMBL3646211	0.8342
14	active_CHEMBL4466555	0.8326
15	active_CHEMBL4583679	0.8322
16	active_CHEMBL4851635	0.8318
17	active_CHEMBL4471379	0.8313
18	active_CHEMBL4081527	0.8303
19	active_CHEMBL4436123	0.8299
20	active_CHEMBL475817	0.8297