Difference between revisions of "User:Mary Mendoza/Notebook/CHEM572 Exp. Biological Chemistry II/2013/02/06"

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==Screening==
 
* Maestro imported structures
 
* Structures were sorted by docking score
 
* Choose molecules with two criteria similarity with aspirin and basis of docking score.
 
* The structures will be chosen with respect to 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 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 14:14, 8 May 2013

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