Molecular Fingerprinting and Docking of Compounds to the ADA active site
A. Opening Maestro
- From the assigned computer, a new terminal was created from either of the following steps:
1. Finder > Services > New terminal at folder
2. press the provided shortcut key F5
- Then enter $maestro to open the suite.
- Draw the molecule on the workspace area. Modifications can be made through the Edit panel > build > fragments > atom properties. Sponge the drawn molecule for clarity.
- To save the molecule, create this entry on the project table -or- from the workspace option > project entry > name and create the project and then save.
- The next step is to put the molecule under energy minimization to find a stable energetically conformation.
B. Energy Minimization
- To initiate energy minimization, go to the Applications option > Impact > Minimization.
- Minimization analyzes the molecule using Classical Physics.
- A dialog box appears with the force field set on OPLS 2005.
- Then click the Minimization tab. On the maximum cycles, this was changed to 10,000. The other standard parameters such as gradient criterion (0.01) and energy change criterion (1e-07) were kept. The pH was changed to the desired pH level of 7.4.
- Knowing there are amino acids present, by changing the pH of the parameters, the structure must also be converted to its alkoxide form at pH 7.4. As a result, through atom types O3 was changed to OM.
- After all the parameters were set for minimization, the host zorro was chosen and the minimization was started.
- Double-click the finished minimization on the monitor jobs (from applications option)