User:Dhea Patel/Notebook/CHEM 572: ADA&Inhibitor Kinetics/2013/01/30: Difference between revisions
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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. | ||
==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 | |||
Revision as of 10:39, 5 February 2013
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Molecular Fingerprinting and Docking of Compounds to the ADA active siteA. Opening Maestro
1. Finder > Services > New terminal at folder -or- 2. press the provided shortcut key F5
|