In this section of this series, I will describe how to find or make a ligand for molecular docking. When we say ‘ligand’ we mean small molecules which could bind to a larger molecule on a specific binding site. It is mostly easy to draw one and obtain the 3D version of the molecule. Sometimes you may want to extract a ligand structure to test your docking suit.
Drawing the molecule:
I used to use Discovery Studio of Biovia (formerly Accelrys) It has a free visualizer. Visualizer could also be used to draw small molecules. After drawing it you can save the file as PDB, MOL2 or their original file format DSV. Especially I very much like the DSV format but AutoDock Suite is not compatible with it. The only option is PDB. If you use Discovery Studio, you have to save your molecule files as PDB.
Unfortunately, this great software does not have a Mac version and I started to sty other options. Even though there are many other tools I am mainly using a web tool. I do not require any installation of very easy to play with. It is MolView.
You can draw any molecule on the canvas and download the 3D version of your molecule with Tools > MOL file path. The resulting file will not be a PDB file. To be able to convert I prefer Open Babel. Open Babel can be used with the command line and for Mac users, iBabel is the available graphical user interface. Even though I prefer the command line version, you can see the iBabel command screen below. You may skip the Open Babel command sand apply what you see on the screenshot.
Open Babel pretends like it can create PDBQT file for us. Do not believe it. The output will be standard PDB file with PDBQT extension. We will create the PDBQT files both for target and ligand in the next section.
NEXT: Obtaining a Ligand Structure