User:Mary Mendoza/Notebook/CHEM572 Exp. Biological Chemistry II/2013/01/30

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(Molecular Fingerprinting and Docking of Compounds to the ADA active site)
Current revision (17:11, 8 May 2013) (view source)
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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 (resolution 2.5 angstroms)
 
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**2Z7G (resolution 2.52 angstroms)
 
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*
 
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