Modeling of mutant
The 1st Anyway, I want to make the mutant model. When the structure has already been analyzed, the PDB file is acquired from structural data. It Homorogamoderings it from the prediction of structure of protein when not analyzed yet.

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. )

Check on structural file
1. Measure/Protein Report is chosen with Sequence Editor.
2. The check on Outliers Only on the right of the Protein Report window is put.
3. Create under the left of the Protein Report window is pushed.
4. Dihedrals, Bond Angles, Bond Lengths, and Contacts are clicked respectively, and the displayed one is seen.
5. The Save button under the Protein Report window is pushed, and the name is preserved specifying it.
6. The file preserved with Wordpad is opened, and printed.

Mutation model
1. The amino acid that wants to mutate is selected with Sequence Editor.
2. Edit/Rotamer Explorer is chosen.
3. The Get from SE button under the left of the Rotamer Explorer window is pushed.
4. The amino acid on the Rotamer Explorer window is changed to the amino acid that wants to mutate and the right Explore is pushed.
5. Mutate at the center under the Rotamer Explorer window is pushed.

Method of examination
1. Check on structural file
2. Check on potential energy. Wild type and comparison.
3. It only has to examine there if it is a mutation model, former structure, and there is a difference.

08/10/09