User:Mary Mendoza/Notebook/CHEM572 Exp. Biological Chemistry II/2013/01/30: Difference between revisions
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* Imported the aspirin.fp molecule and allow duplicate mappings. | * Imported the aspirin.fp molecule and allow duplicate mappings. | ||
* Go to the Applications > similar/distance screen > select aspirin. | * Go to the Applications > similar/distance screen > select aspirin. | ||
** Tanimoto similarity | |||
* Selected the fingerprint column and choose the fingerprint (aspirin) | * Selected the fingerprint column and choose the fingerprint (aspirin) | ||
* Screened the molecules and then incorporate ~ 15,001 | * Screened the molecules and then incorporate ~ 15,001 | ||
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E. Docking | E. Docking | ||
[[Image:Prepwizard2.png|thumb|right|Protein Preparation Wizard_Import and Process Tab]] | |||
* Opened the protein databank (PDB) website, www.rcsb.org, and acquired two ADA Bovine structures. The two following structures were chosen by desirable resolutions: | * 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 | **1KRM (resolution 2.5 angstroms) | ||
**2Z7G (resolution 2.52 angstroms) | |||
** | * The pdb.txt of these structures were downloaded. | ||
* 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 | |||
[[Image:Refine75.png]] | |||
* After Optimization, | |||
Revision as of 13:12, 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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