Objective

To dock biotin into the streptavidin receptor.

Instructions

• Docking/Set Project Name (BIOTIN)

• Docking/Load Example (streptavidin complexed with haba)
• Select biotin in workspace window and right click and select neighbors.

• Select atoms on other objects in a 5 A radius.
• Docking/Receptor setup (Receptor molecules: a_rec.a)

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:

• Docking/Ligand Setup/From Loaded ICM object (Ligand molecule: a_biotin.biotin)

Now let us make the maps - this may take a few minutes.

• Docking/Make Receptor Maps

To start the docking simulation:

• Docking/interactive docking/loaded ligand (Ligand object: a_biotin.)

Once the simualtion has finished select

• MolMechanics > View Stack
• Double click on each element of the stack and the ligand will be displayed in the graphical display. Each ligand position can be displayed or undisplayed using the ICM workspace.