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==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
 
 
-or-
 
 
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), 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
 
* Click on the imported molecule and incorporate.
 
* Export the molecule by saving it with an extension of .fp
 
* A dialog box will appear, choose remove all properties and click ok.
 
* Close the project.
 
 
 
D. Screen Fingerprint
 
 
* After closing the previous aspirin project, open the zinc database.
 
* Imported the aspirin.fp molecule and allow duplicate mappings.
 
* Go to the Applications > similar/distance screen > select aspirin.
 
*** Tanimoto similarity
 
* Selected the fingerprint column and choose the fingerprint (aspirin)
 
* Screened the molecules and then incorporate ~ 15,001
 
* Clicked the fingerprint screen column and sort in descending order to show molecules closest to aspirin.
 
* On the panel, select rows 1-15,001
 
* Saved the selection by exporting the project as aspirin_15001.mae along with its properties and click OK.
 
* Closed Canvas
 
 
 
E. Docking
 
 
* Opened the protein databank (PDB) website, www.rcsb.org, and acquired two ADA Bovine structures. The two following structures were chosen by desirable resolutions:
 
****1KRM
 
****2Z7G
 
 
*
 
 
  
  

Latest revision as of 22:24, 26 September 2017

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