User:Mary Mendoza/Notebook/CHEM572 Exp. Biological Chemistry II/2013/01/30: Difference between revisions
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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: | ||
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* 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 | |||
Revision as of 22:08, 7 February 2013
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> </html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html> |
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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