Difference between revisions of "User:Dhea Patel/Notebook/CHEM 572: ADA&Inhibitor Kinetics/2013/02/06"

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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Project name</span>
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|colspan="2" style="background-color: #F2F2F2;" align="right"|[[{{FULLPAGENAME}}/Entry_Base|Customize your entry pages]] [[Image:Help.png|frameless|link=Help:Notebook/Project_Base/Customize_entry_page]]
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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.
  
==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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Latest revision as of 17:57, 23 September 2017

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Customize your entry pages Help.png

taken from Mary's Notebook. We performed all the following steps together.