Rank an Output File of Ligands

Sometimes, after you do a docking of your protein of interest with a bunch of ligands, exist the needs of  rank this ones by energies of interaction. In Dock6 exist an option in the input file that permit us to do this. The option is called rank_ligands, and only to choose the "yes" option you will get your ligands ranked. But in other cases (like the one happened to me) you forgot to choose that option. 

I create a python code that let you to rank the ligands that you want (i.e the first 1000) and gives you an output of only your top ligands. It's somewhat limited, because only accept files in mol2 format and can order molecules that you obtain from ZINC database.

How the program works

The program will ask you 2 questions. The first one is related to the name of your file. Write it without the extension, because the program assume that the file is in mol2 format. The second question is the number of ligands that you want to rank. If you want to rank the better 1000 ligands just write 1000.

Supported format for RankDock

RankDock.py

Simple Docking Calculations with Dock6

The molecular docking is a powerful tool that allows us to analyze the orientation of any ligand or protein against some target, which is usually a protein.

Docking of a ligand into the cavity of a protein.

There are several programs for docking calculations. I have personally used the program Dock6. This program takes 3 initial files: Our receptor in .mol2 format, our ligand or ligands in .mol2 format, and a receptor surface file in .dms format. mol2 files must have hydrogens and molecular charge . For this I use the program Chimera, and transformed my PDB files as shown here (http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecules.html). dms file can be built with the WriteDMS program included in Chimera.

With these files , the next steps are to create spheres surrounding the receptor, select a group of spheres that represent the binding site, build a box around the binding site, and grid generation. The tutorial mentioned above explains in detail the steps to follow. I built a program called Do_Dock6.py that allows us to perform all these steps in a simple and guided . You only need to have the files of the receptor and ligand, and the dms file, all these generated in Chimera.

How the program works

The program performs certain questions. Answer each question according to the location of your files. I recommend making a folder ( ie " DOCK / " ) where you keep your files mol2 and dms. After you create your spheres (saved in a folder named "SHOWSPH") the next question it is if you want to calculate the grid. Before doing this, you have to open all your sphere files (named like cluster_1, cluster_2, etc) and your box files (saved in a folder named "REC_BOX") in a molecular viewer like PyMol. Search the cluster and the box that fits well with your needs. Then run the program again and choose "N" in the question about sphere generation. When the question about grid calculation appears, choose "Y" and continue.

All box visualization.

Sphere and box visualization.

Do_dock6.py