Arguslab

There are many types of Computer Aided Drug-Design (CADD) nowadays. One of it is Argus Lab. Argus Lab is authored by a scientist and scientist software developer in the theoretical and computational chemistry field, Mark Thompson. It is a molecular modeling, graphics, and drug design program for electronic devices that use Windows operating systems. 

Its work by using new algorithms for modeling solvent effects by combining quantum mechanics with classical mechanics. These methods were used to simulate molecules that bind radionuclides from complex waste which is useful for drug design.

This type of CADD is currently used by scientists and students worldwide. ArgusLab is favourable because of its many advantages. Although it is quite a little dated by now, yet surprisingly still remains as one of the most popular CADD among the users. There are more than 20,000 downloads to date. 

This software is very convenient since the user can download and use it without license. However, the user is restricted from redistributing this from other website or sources. Specifically, this application software will helps us to calculate the docking affinity. Let us see how ArgusLab helps us in designing a drug! 

For example if we want to dock benzadymine molecule (inhibitor) into beta trypsin. It will helps us to calculate dock affinity of a ligand into its binding site. First of all, we need to make up the component of the ligand and the binding site. So, we are going to use the structure from online database which is Brookehaven Protein Data Bank (RCSB PDB). The PDB will looks as follows :

Then, go to the search box on the upper right and search for benzamidine and open the structure file. Next, open the protein data bank file and make sure the format is PDB file.

Make sure the Molecule Tree View is visible and expand it all. You should see something like this.

Then the screen will be showing the benzamidine molecule. Now, we can add hydrogen atom to the benzamidine molecule by clicking the ribbon button on the upper part.

The silver part is the hydrogen atom that being added to the molecule.

Now, we are going to make the copy of this molecule. There will be two groups of molecule which are ligand and its binding site. 

This will appear on your screen. Okay now its time to dock the ligand into the binding site! A table will appear upon clicking. We must make sure the the binding site bounding box is filled correctly. Then, set the required grid resolution. After all is complete, click start button and the system will start calculate the binding affinity between ligand and its binding site for you. The value will be showed in the diagram as below.

So, that is how ArgusLab helps us in drug design. The scientist and student worldwide are using this type of CADD to develop a new drug. This is one of their way to choose the most potential lead compound. Obviously, this application is very effective and efficient