A molecular modeling, graphics, and drug design program. ArgusLab is a very useful, highly-featured and easy-to-use molecular modeling. Arguslab offers quite good on-screen molecule-building facilities, with a moderate library of useful molecules. The viewer is mouse-controlled quite similarly to. Tutorial. Molecular Docking Using ArgusLab (4ACM). Prof. Dr. Walter Filgueira de Azevedo Jr. [email protected] 1. Introduction. Docking .
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Documents Flashcards Grammar checker. Table of Contents or Index Entry Information 1 de 3 http: You argulab have worked through the benzamidine-beta trypsin tutorial before running this tutorial. In this tutorial you will learn: How to run docking calculations using a ligand stored in a file separate from the protein target file.
How to visualize hydrogen bonds between ligands and protein targets. Explore ribbon rendering of the protein that enhance your ability to understand their arhuslab. Open the structure file. Open the protein databank file, 1 hvr.
This is an ArgusLab file which I’ve prepared for you. It contains the inhibitor XK from the original x-ray structure. The XK is already defined as a Ligand and the binding site has been made. Only the ligand and binding site atoms are visible when the structure comes up on the screen. Make sure the Molecule Tree View tool is visible.
You should see something like this: Table of Contents or Index Entry Information 2 de 3 http: Examine the hydrogen bonding in the x-ray structure. Right-click on the “XK2-xray” ligand, in the Groups folder, and select “Show hydrogen bonds”.
You should see several red-lines appear between the XK ligand and the protein. These are the hydrogen bonds between ligand and protein. Zoom the structure to bring some of the h-bonds into clearer view. Right-click on one of the red-lines and select “Hydrogen bond info This will bring up an info dialog with information about this particular h-bond. Notice that there are good hydrogen bonds between the two hydroxyl groups of the cyclic urea ring and the two catalytic aspartic acid residues Asp and Asp 25 andand between the keto group of the cyclic urea and the peptide nitrogen of Ile Try changing the color of the h-bonds.
If you change the h-bond distance value, you will then need to remove the h-bonds and re-calculate them. Dock another copy of XK into the binding site. Open the file xk I have already created a Ligand Group for this structure and you should verify this by looking in the Groups folder under the xk molecule in the Tree View.
Set the Binding Site Bounding Box size to 18, 18, 22 Angstroms for x,y,z respectively, by typing these dimensions into the edit boxes. Make sure ArgusDock is the docking engine, the calc type tutoral Dock, and the Ligand is flexible options are selected. This newly added ligand will then be docked. The final result is 1 hvr containing the additional ligand. You can dock multiple ligands from multiple sources into any molecule that has a binding site defined, thus allowing for the overlapping of multiple ligands to see common modes of binding, etc.
Argus SAF – Argus-PAG
Right-click on the binding site in the Groups folder and select the “Hide” option. Do the same thing for the “XK2-xray” ligand. Now only the newly docked “XK inhibitor” is visible.
Tuforial on “XK inhibitor” and select “Show Hydrogen Bonds” You should see just the ligand and several lines emanating from it.
Tutorial Molecular Docking: HIV Protease inhibitor XK263
If you want to see just the protein residues that participate in the h-bonds, right click on any h-bond line and select the “Show All Hydrogen Bonds’ Residues” option. This will make just the h-bonding residues from the target visible along with the already visible ligand. Note that these are essentially the same as the x-ray ligand’s h-bonds. Viewing the protein with ribbons. HIV protease is a homo-dimeric enzyme. You can visualize the overall structure of the entire protein ligand complex by rendering the protein with ribbons turned on.
You may have to zoom the structure out a bit to get it all on the graphics screen. Notice, also, how the two catalytic aspartic acid residues come from analogous positions on each of the two subunits.
Questions on Peng, Yutorial. In the diagram below, the d orbital splitting diagrams are given for 6. Computational modeling of the copper. Self-assembly, Ligand activity and Molecular delivery.