User:Mary Mendoza/Notebook/CHEM572 Exp. Biological Chemistry II/2013/01/30 - Revision history

Mary Mendoza: /* Notes */

Mary Mendoza — Wed, 08 May 2013 22:11:46 GMT

Notes

←Older revision		Revision as of 22:11, 8 May 2013
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-	~~==Notes==~~
-
-	* The database chosen were compounds that did not cross the Blood Brain Barrier.

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Mary Mendoza: /* Molecular Fingerprinting of Compounds to the ADA active site */

Mary Mendoza — Wed, 08 May 2013 22:11:25 GMT

Molecular Fingerprinting of Compounds to the ADA active site

←Older revision		Revision as of 22:11, 8 May 2013
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-	~~==Molecular Fingerprinting of Compounds to the ADA active site==~~
-	* The objective for this laboratory period is obtain the molecular fingerprint of aspirin and dock compounds to the binding pocket of adenosine deaminase (ADA).

-
-	~~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.
-	** Force field is a set of rules containing how atom types are connected angle and torsional angle
-	** gives the constant measure of force
-	** The Constraints tab contain NOE, NMR, indicating the closeness of atoms and information about the radius
-	* 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.
-	** A noticeable common feature among the imported database is the benzene ring.
-	* Closed Canvas
-
-
-	~~E. Docking Preparation~~
-	~~[[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
-
-	~~[[Image:Refine75.png\|center]]~~
-
-
-	~~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.
-	* Compared both structures by superimposing them.
-	* Verified structure 1KRM has a better resolution and removed 2Z7G from the project table.
-	* Showed ribbons for 1KRM and colored element entry carbons
-
-
-	~~G. Docking~~
-	* Duplicated the 1KRM H-minimized and deleted water molecules by manually clicking on each.
-	** Removed the water molecules to remove the rigidity of the protein. This also interferes with the docking of compounds by taking up space.
-	* Changed ribbon color by residue position
-	* Made a grid of the docking region by:
-	** Application > Glide > Receptor Grid Generation
-	** Select the ligand
-	** Click site tab > center on ligand > change dock ligands to 15 Angstroms
-	** Click Start
-	* Changed the grid name and specified the host: zorro; click OK
-
-
-	* Seeing the docking is done from the Monitor Jobs window:
-	** Applications > Glide > Ligand Docking
-	** Browse for the .zip grid previously created
-	** Verify host: zorro and click start
-	* Imported the glide.pv file
-	* Excluded the protein structure leaving only the ligand
-	* Superimposed the raw, crystallized PDB ADA ligand structure with the docked ligand
-	* Imported flavonoids to compare with the docked ligand by superimposition
-	* Database screening was initiated by going to Applications > Glide > Ligand Docking
-	* Selected the entry with 15,000 compounds from the .pv file
-	* Selected zorro host and clicked start

	==Notes==		==Notes==

Mary Mendoza: /* Molecular Fingerprinting of Compounds to the ADA active site */

Mary Mendoza — Fri, 08 Feb 2013 15:48:52 GMT

Molecular Fingerprinting of Compounds to the ADA active site

←Older revision		Revision as of 15:48, 8 February 2013
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	==Molecular Fingerprinting of Compounds to the ADA active site==		==Molecular Fingerprinting of Compounds to the ADA active site==
		+	* The objective for this laboratory period is obtain the molecular fingerprint of aspirin and dock compounds to the binding pocket of adenosine deaminase (ADA).
		+

	A. Opening Maestro		A. Opening Maestro
Line 118:		Line 120:
	* Selected the entry with 15,000 compounds from the .pv file		* Selected the entry with 15,000 compounds from the .pv file
	* Selected zorro host and clicked start		* Selected zorro host and clicked start
-

	==Notes==		==Notes==

Mary Mendoza: /* Molecular Fingerprinting of Compounds to the ADA active site */

Mary Mendoza — Fri, 08 Feb 2013 05:46:51 GMT

Molecular Fingerprinting of Compounds to the ADA active site

←Older revision		Revision as of 05:46, 8 February 2013
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	* Minimization analyzes the molecule using Classical Physics.		* Minimization analyzes the molecule using Classical Physics.
	* A dialog box appears with the force field set on OPLS 2005.		* A dialog box appears with the force field set on OPLS 2005.
		+	** Force field is a set of rules containing how atom types are connected angle and torsional angle
		+	** gives the constant measure of force
		+	** The Constraints tab contain NOE, NMR, indicating the closeness of atoms and information about the radius
	* 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.		* 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.		* 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.
Line 59:		Line 62:
	* On the panel, select rows 1-15,001		* 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.		* Saved the selection by exporting the project as aspirin_15001.mae along with its properties and click OK.
		+	** A noticeable common feature among the imported database is the benzene ring.
	* Closed Canvas		* Closed Canvas

Line 93:		Line 97:
	G. Docking		G. Docking
	* Duplicated the 1KRM H-minimized and deleted water molecules by manually clicking on each.		* Duplicated the 1KRM H-minimized and deleted water molecules by manually clicking on each.
		+	** Removed the water molecules to remove the rigidity of the protein. This also interferes with the docking of compounds by taking up space.
	* Changed ribbon color by residue position		* Changed ribbon color by residue position
	* Made a grid of the docking region by:		* Made a grid of the docking region by:
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		+	==Notes==

		+	* The database chosen were compounds that did not cross the Blood Brain Barrier.

	<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->		<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->

Mary Mendoza: /* Molecular Fingerprinting of Compounds to the ADA active site */

Mary Mendoza — Fri, 08 Feb 2013 05:36:14 GMT

Molecular Fingerprinting of Compounds to the ADA active site

←Older revision		Revision as of 05:36, 8 February 2013
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	** Click Start		** Click Start
	* Changed the grid name and specified the host: zorro; click OK		* Changed the grid name and specified the host: zorro; click OK
		+

	* Seeing the docking is done from the Monitor Jobs window:		* Seeing the docking is done from the Monitor Jobs window:
Line 112:		Line 113:
	* Selected the entry with 15,000 compounds from the .pv file		* Selected the entry with 15,000 compounds from the .pv file
	* Selected zorro host and clicked start		* Selected zorro host and clicked start
-
-

Mary Mendoza: /* Molecular Fingerprinting and Docking of Compounds to the ADA active site */

Mary Mendoza — Fri, 08 Feb 2013 05:34:50 GMT

Molecular Fingerprinting and Docking of Compounds to the ADA active site

←Older revision		Revision as of 05:34, 8 February 2013
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-	==Molecular Fingerprinting ~~and Docking~~ of Compounds to the ADA active site==	+	==Molecular Fingerprinting of Compounds to the ADA active site==

	A. Opening Maestro		A. Opening Maestro
Line 100:		Line 100:
	** Click Start		** Click Start
	* Changed the grid name and specified the host: zorro; click OK		* Changed the grid name and specified the host: zorro; click OK
		+
		+	* Seeing the docking is done from the Monitor Jobs window:
		+	** Applications > Glide > Ligand Docking
		+	** Browse for the .zip grid previously created
		+	** Verify host: zorro and click start
		+	* Imported the glide.pv file
		+	* Excluded the protein structure leaving only the ligand
		+	* Superimposed the raw, crystallized PDB ADA ligand structure with the docked ligand
		+	* Imported flavonoids to compare with the docked ligand by superimposition
		+	* Database screening was initiated by going to Applications > Glide > Ligand Docking
		+	* Selected the entry with 15,000 compounds from the .pv file
		+	* Selected zorro host and clicked start

Mary Mendoza: /* Molecular Fingerprinting and Docking of Compounds to the ADA active site */

Mary Mendoza — Fri, 08 Feb 2013 05:08:02 GMT

Molecular Fingerprinting and Docking of Compounds to the ADA active site

←Older revision		Revision as of 05:08, 8 February 2013
Line 62:		Line 62:


-	E. Docking	+	E. Docking Preparation
	[[Image:Prepwizard2.png\|thumb\|right\|Protein Preparation Wizard_Import and Process Tab]]		[[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:
Line 86:		Line 86:
	* Added ribbons for all residues to view the entire structure		* 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.		* Upon scanning the structure, subtracted all portions leaving only the ligand on display at 5 Angstroms.
-	*	+	* Compared both structures by superimposing them.
		+	* Verified structure 1KRM has a better resolution and removed 2Z7G from the project table.
		+	* Showed ribbons for 1KRM and colored element entry carbons
		+
		+
		+	G. Docking
		+	* Duplicated the 1KRM H-minimized and deleted water molecules by manually clicking on each.
		+	* Changed ribbon color by residue position
		+	* Made a grid of the docking region by:
		+	** Application > Glide > Receptor Grid Generation
		+	** Select the ligand
		+	** Click site tab > center on ligand > change dock ligands to 15 Angstroms
		+	** Click Start
		+	* Changed the grid name and specified the host: zorro; click OK
		+
		+
		+
		+

Mary Mendoza: /* Molecular Fingerprinting and Docking of Compounds to the ADA active site */

Mary Mendoza — Fri, 08 Feb 2013 04:48:57 GMT

Molecular Fingerprinting and Docking of Compounds to the ADA active site

←Older revision		Revision as of 04:48, 8 February 2013
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	** Then click Optimize		** Then click Optimize

-	[[Image:Refine75.png]]	+	[[Image:Refine75.png\|center]]

Mary Mendoza: /* Molecular Fingerprinting and Docking of Compounds to the ADA active site */

Mary Mendoza — Fri, 08 Feb 2013 04:48:16 GMT

Molecular Fingerprinting and Docking of Compounds to the ADA active site

←Older revision		Revision as of 04:48, 8 February 2013
Line 79:		Line 79:


-	* After Optimization,	+	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.
		+	*

Mary Mendoza: /* Molecular Fingerprinting and Docking of Compounds to the ADA active site */

Mary Mendoza — Wed, 06 Feb 2013 20:12:05 GMT

Molecular Fingerprinting and Docking of Compounds to the ADA active site

←Older revision		Revision as of 20:12, 6 February 2013
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	** Moving to the Refine Tab, changed the default pH of 7.0 to 7.4 as shown below.		** Moving to the Refine Tab, changed the default pH of 7.0 to 7.4 as shown below.
	** Then click Optimize		** Then click Optimize
-	** After optimization

	[[Image:Refine75.png]]		[[Image:Refine75.png]]

		+
		+	* After Optimization,