User:Mary Mendoza/Notebook/CHEM572 Exp. Biological Chemistry II/2013/01/30: Difference between revisions
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* Created a new project and named it as Aspirin_fingerprint. | * Created a new project and named it as Aspirin_fingerprint. | ||
* Imported the energy minimized aspirin saved earlier from maestro. | * Imported the energy minimized aspirin saved earlier from maestro. | ||
* Under applications option, click binary fingerprints > molprint2D | * Under applications option, click binary fingerprints > molprint2D | ||
* Click on the imported molecule and incorporate. | * Click on the imported molecule and incorporate. | ||
* Export | * Export the molecule by saving it with an extension of .fp | ||
* A dialog box will appear, choose remove all properties and click ok. | |||
* Close the project. | |||
D. Screen Fingerprint | |||
* After closing the previous aspirin project, open the zinc database. | |||
* Imported the aspirin.fp molecule and allow duplicate mappings. | |||
* Go to the Applications > similar/distance screen > select aspirin. | |||
** Tanimoto similarity | |||
* Selected the fingerprint column and choose the fingerprint (aspirin) | |||
* Screened the molecules and then incorporate ~ 15,001 | |||
* Clicked the fingerprint screen column and sort in descending order to show molecules closest to aspirin. | |||
* On the panel, select rows 1-15,001 | |||
* Saved the selection by exporting the project as aspirin_15001.mae along with its properties and click OK. | |||
* Closed Canvas | |||
E. Docking | |||
* Opened the protein databank (PDB) website, www.rcsb.org, and acquired two ADA Bovine structures. The two following structures were chosen by desirable resolutions: | |||
**1KRM (resolution 2.5 angstroms) | |||
**2Z7G (resolution 2.52 angstroms) | |||
* The pdb.txt of these structures were downloaded. | |||
[[Image:Prepwizard2.png|thumb|right|Protein Preparation Wizard_Import and Process Tab]] | |||
* On Maestro, opened the aspirin.prj and imported the downloaded structures of ADA. | |||
* The structures of ADA were protonated according to the pH of 7.4. This was executed from: | |||
** Workflows > Protein preparation Wizard | |||
** On the Import and Process Tab, add H<sup>+</sup> (see image on the right side of the protein preparation wizard dialog box) | |||
** Uncheck the delete waters on the dialog box and click preprocess. | |||
** Moving to the Refine Tab, changed the default pH of 7.0 to 7.4 as shown below. | |||
** Then click Optimize | |||
** After optimization | |||
[[Image:Refine75.png]] | |||
Revision as of 13:07, 6 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
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