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22.7 Ligand Docking Tutorials
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[ Re-Dock Biotin to the Streptavidin Receptor | Re-Dock an Inhibitor to Ricin Crystal Structure ]

22.7.1 Re-Dock Biotin to the Streptavidin Receptor


Objective

To dock biotin into the streptavidin receptor.

Instructions

The binding pocket should be displayed something like as shown below:

In the terminal window instructions will be given telling you how to alter the initial starting position of the ligand and how to change the size of the box in which the maps will be generated.

Adjust box size / probe position and press return or use the green GO button in the bottom left hand corner.

Now let us set up the ligand and start the simulation:

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Once the simualtion has finished select

22.7.2 Re-Dock an Inhibitor to Ricin Crystal Structure


Objective

To re-dock a ricin inhibitor into the ricin crystal structure (1br6).

Instructions

NOTE: The simulation may take longer if you are displaying the ligand during docking.

Once the docking has finished you can display the best energy solution

Compare with crystal structure


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