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

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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.
*Taken from [[User:Mary_Mendoza/Notebook/CHEM572_Exp._Biological_Chemistry_II/2013/01/30|Mary's Notebook]]. We did all the steps together.
*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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==Opening Maestro==
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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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#From the assigned computer, a new terminal was created by either:
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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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##Finder > Services > New terminal at folder OR
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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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##press the provided shortcut key F5
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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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#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.

Revision as of 14:10, 6 February 2013

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Objective

  • to use Maestro and Canvas to calculate molecular fingerprints and docking scores of various commercial compounds in relation to the ADA active site.

Opening Maestro

  1. From the assigned computer, a new terminal was created by either:
    1. Finder > Services > New terminal at folder OR
    2. press the provided shortcut key F5
  2. Then, enter $maestro to open the suite.
  3. Draw the molecule on the workspace area.
    1. Modifications can be made through the Edit panel > build > fragments > atom properties.
    2. Sponge the drawn molecule for clarity.
  4. Save the molecule:
    1. create this entry on the project table OR
    2. Workspace option > project entry > name and create the project and then save.
  5. 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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