- to use Maestro and Canvas to calculate molecular fingerprints and docking scores of various commercial compounds in relation to the ADA active site.
- From the assigned computer, a new terminal was created by either:
- Finder > Services > New terminal at folder OR
- 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.
- Save the molecule:
- create this entry on the project table OR
- Workspace option > project entry > name and create the project and then save.
- 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), then label the partial charges of the molecule.
- Save the project entry.
C. Calculation of Fingerprint
- Opened Canvas from the Finder by typing $Canvas
- Created a new project and named it as Aspirin_fingerprint.
- Imported the energy minimized aspirin saved earlier from maestro.
- Under applications option, click binary fingerprints > molprint2D and create.
- Click on the imported molecule and incorporate.