Difference between revisions of "User:Mary Mendoza/Notebook/CHEM572 Exp. Biological Chemistry II/2013/01/30"

From OpenWetWare
(Molecular Fingerprinting and Docking of Compounds to the ADA active site)
(7 intermediate revisions by the same user not shown)
Line 6: Line 6:
| colspan="2"|
| colspan="2"|
<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
==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
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
* Click on the imported molecule and incorporate.
* 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
[[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:
**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
F. Superimposition of Proteins
* After Optimization, navigated through Tools > Protein Structure Alignment
** All > align
** From the Undisplay icon, remove waters for both structures
* Added ribbons for all residues to view the entire structure
* Upon scanning the structure, subtracted all portions leaving only the ligand on display at 5 Angstroms.

Revision as of 15:11, 8 May 2013

Owwnotebook icon.png Project name <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>