User:Dhea Patel/Notebook/CHEM 572: ADA&Inhibitor Kinetics/2013/02/06

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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.
taken from [[User:Mary_Mendoza/Notebook/CHEM572_Exp._Biological_Chemistry_II/2013/02/06|Mary's Notebook]]. We performed all the following steps together.
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==Screening==
 
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* 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.
 
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* Opened Maestro and imported the docked structures from last week.
 
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* Structures were sorted by docking score
 
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* The molecules were chosen based on two criteria, (1) similarity with aspirin and (2) basis of docking score.
 
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* The similarity of compounds to aspiring is indicated by the Tanimoto coefficient.
 
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* On the workspace, observed the structures with its bonding to the amino acids located on the binding pocket.
 
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* Molecules with Arginine bind best to the carboxylate of the amino acids.
 
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* Some molecules are efficient in terms of geometry and size but exhibit few hydrogen bonds.
 
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* Under the property options > show all
 
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* Select the fpscreen_01-1, sorted by the Tanimoto coefficient.
 
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* 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.
 
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* Some molecules have high docking scores but do not have affinity to the binding pocket. Thus, docking scores are unreliable for this circumstance.
 
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* After selecting the molecules, the structures were viewed under 2D Sketcher.
 
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* The zinc ID number for each structure were entered to the zinc website to verify its availability for purchase.
 
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* The table of structures were exported to excel to view the vendor list.
 
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* Eight structures were chosen based on their docking score and five for their similarity to aspirin.
 
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* The final list of structures were uploaded into dropbox and posted below.
 
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[[Image:Struc1.png|center]]
 
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[[Image:Orderlist.png]]
 
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taken from Mary's Notebook. We performed all the following steps together.



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