User:Dhea Patel/Notebook/CHEM 572: ADA&Inhibitor Kinetics/2013/02/06: Difference between revisions
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taken from [[User:Mary_Mendoza/Notebook/CHEM572_Exp._Biological_Chemistry_II/2013/02/06|Mary's Notebook]]. We performed all the following steps together. | |||
==Screening== | |||
* The objective of screening compounds for this laboratory period is to obtain a list of compounds that would be ordered and investigated for this project. | |||
* Opened Maestro and imported the docked structures from last week. | |||
* Structures were sorted by docking score | |||
* The molecules were chosen based on two criteria, (1) similarity with aspirin and (2) basis of docking score. | |||
* The similarity of compounds to aspiring is indicated by the Tanimoto coefficient. | |||
* On the workspace, observed the structures with its bonding to the amino acids located on the binding pocket. | |||
* Molecules with Arginine bind best to the carboxylate of the amino acids. | |||
* Some molecules are efficient in terms of geometry and size but exhibit few hydrogen bonds. | |||
* Under the property options > show all | |||
* Select the fpscreen_01-1, sorted by the Tanimoto coefficient. | |||
* Compared the docking score and the Tanimoto coefficient. Most scores were low as expected. Molecules that had docking scores averaging between 7-8 were considered alongside its Tanimoto coefficient. | |||
* Some molecules have high docking scores but do not have affinity to the binding pocket. Thus, docking scores are unreliable for this circumstance. | |||
* After selecting the molecules, the structures were viewed under 2D Sketcher. | |||
* The zinc ID number for each structure were entered to the zinc website to verify its availability for purchase. | |||
* The table of structures were exported to excel to view the vendor list. | |||
* Eight structures were chosen based on their docking score and five for their similarity to aspirin. | |||
* The final list of structures were uploaded into dropbox and posted below. | |||
[[Image:Struc1.png|center]] | |||
[[Image:Orderlist.png]] | |||
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Revision as of 10:31, 8 February 2013
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taken from Mary's Notebook. We performed all the following steps together. Screening
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