Docking
Acquisition of PDB file
Optimization of PDB file
1. MOE is started.
2. It opens with File/Open.
Right Force Type is made PDB for PDB file after the file is selected and OK is pushed. Afterwards, OK is pushed twice.
3. The 2nd and Sequence Editor of the button on the right of the window are opened.
4. Chain such as H2O and Rigand is pushed when the item of Chain of the Sequence Editor window is not one, and it deletes it with Edit/Delete Selected Chain.
5. Select/Element/Heavy Atom is chosen.
6. Edit/Fix is chosen.
7. Compute/Energy Minimize is chosen. The figure appears on the left, and it ends after a while.
8. The file name is preserved with File/Save specifying it. The file attribute. It is comprehensible when putting it as moe.
(The potential energy is recorded because it uses it later. )
Acquisition of Rigand
a. Refer to attachment CD to Yoot "Moving molecular dictionary consulted with the personal computer" Honma and riverside Ul of Blubaccs.
b. It obtains it by the Internet.
C.SciFinder Scholar is used.
d. It obtains it from the compound data base.
e. Build is done for myself and it optimizes it.
Docking simulation
1. MOE is started.
2. It opens with File/Open.
3. The 2nd and Sequence Editor of the button on the right of the window are opened.
4. It is a choices mouse right-clicking and Atoms/Select as for chain of Rigand.
Menu..input..column..input..return.
Even the calculation end is waited for. Because the file of method mdb of the examination is made, and the state is displayed as some candidates, each item is examined. To know the interaction energy, it is displayed that the Rigand molecule is selected, and it is assumed MOE/Compute/Ptential energy in the upper part of the screen.

08/10/09