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

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==Entry title==
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* Insert content here...
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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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==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 and create.
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* Click on the imported molecule and incorporate.
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* Export
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Revision as of 13:39, 5 February 2013

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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 and create.
  • Click on the imported molecule and incorporate.
  • Export




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