User:Dhea Patel/Notebook/CHEM 572: ADA&Inhibitor Kinetics/2013/01/30

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(Opening Maestro)
 
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==Objective==
 
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*to use Maestro and Canvas to calculate molecular fingerprints and docking scores of various commercial compounds in relation to the ADA active site.
 
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*Taken from [[User:Mary_Mendoza/Notebook/CHEM572_Exp._Biological_Chemistry_II/2013/01/30|Mary's Notebook]]. We did all the steps together.
 
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==Opening Maestro==
 
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#From the assigned computer, a new terminal was created by either:
 
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##Finder > Services > New terminal at folder OR
 
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##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.
 
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##Modifications can be made through the Edit panel > build > fragments > atom properties.
 
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##Sponge the drawn molecule for clarity.
 
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#Save the molecule:
 
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##create this entry on the project table OR
 
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##Workspace option > project entry > name and create the project and then save.
 
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#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 and create.
 
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* Click on the imported molecule and incorporate.
 
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* Export
 

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