User:Mary Mendoza/Notebook/CHEM572 Exp. Biological Chemistry II/2013/01/30: Difference between revisions
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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 | ||
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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. | ||
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* 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 | ||
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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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* Selected zorro host and clicked start | * Selected zorro host and clicked start | ||
==Notes== | |||
* The database chosen were compounds that did not cross the Blood Brain Barrier. | |||
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Revision as of 08:48, 8 February 2013
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Molecular Fingerprinting of Compounds to the ADA active site
1. Finder > Services > New terminal at folder -or- 2. press the provided shortcut key F5
Notes
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