arguslab实例.docVIP

Molecular Docking: HIV Protease inhibitor XK263 Prerequisite:? You should 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 structure. The structure files you will need are in the ArgusLab40/Tutorials/Docking/HIV Protease folder.?? ? 1. Open the structure file. Open the protein databank file, 1hvr.agl located in the Tutorials/Docking/HIV Protease folder of your ArgusLab installation.? This is an ArgusLab file which Ive prepared for you.? It contains the inhibitor XK263 from the original x-ray structure.? The XK263 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.? Either select Tools/Molecule Tree View menu option or click the?button on the toolbar to toggle the Tree View. Expand the tree view of 1hvr and confirm for yourself that the proper groups have been defined..? You should see something like this: ? 2. 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 XK263 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 125 and Asp 25) a