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| ==Molecular Fingerprinting and Docking of Compounds to the ADA active site==
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| A. Opening Maestro
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| * From the assigned computer, a new terminal was created from either of the following steps:
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| 1. Finder > Services > New terminal at folder
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| -or-
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| 2. press the provided shortcut key F5
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| * Then enter $maestro to open the suite.
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| * 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.
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| * 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.
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| * The next step is to put the molecule under energy minimization to find a stable energetically conformation.
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| B. Energy Minimization
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| * To initiate energy minimization, go to the Applications option > Impact > Minimization.
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| * Minimization analyzes the molecule using Classical Physics.
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| * A dialog box appears with the force field set on OPLS 2005.
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| * 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.
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| * 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.
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| * After all the parameters were set for minimization, the host zorro was chosen and the minimization was started.
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| * Double-click the finished minimization on the monitor jobs (from applications option), then label the partial charges of the molecule.
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| * Save the project entry.
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| C. Calculation of Fingerprint
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| * Opened Canvas from the Finder by typing $Canvas
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| * Created a new project and named it as Aspirin_fingerprint.
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| * Imported the energy minimized aspirin saved earlier from maestro.
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| * Under applications option, click binary fingerprints > molprint2D
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| * Click on the imported molecule and incorporate.
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| * Export the molecule by saving it with an extension of .fp
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| * A dialog box will appear, choose remove all properties and click ok.
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| * Close the project.
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| D. Screen Fingerprint
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| * After closing the previous aspirin project, open the zinc database.
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| * Imported the aspirin.fp molecule and allow duplicate mappings.
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| * Go to the Applications > similar/distance screen > select aspirin.
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| *** Tanimoto similarity
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| * Selected the fingerprint column and choose the fingerprint (aspirin)
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| * Screened the molecules and then incorporate ~ 15,001
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| * Clicked the fingerprint screen column and sort in descending order to show molecules closest to aspirin.
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| * On the panel, select rows 1-15,001
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| * Saved the selection by exporting the project as aspirin_15001.mae along with its properties and click OK.
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| * Closed Canvas
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| E. Docking
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| * Opened the protein databank (PDB) website, www.rcsb.org, and acquired two ADA Bovine structures. The two following structures were chosen by desirable resolutions:
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| **1KRM
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| **2Z7G
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| *
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Project name
