User:Mary Mendoza/Notebook/CHEM572 Exp. Biological Chemistry II/2013/02/06

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(Computational Screening)
Current revision (17:14, 8 May 2013) (view source)
(Screening)
 
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==Computational Screening==
 
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* Maestro imported structures
 
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* Structures were sorted by docking score
 
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* Choose molecules with two criteria similarity with aspirin and basis of docking score.
 
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* The structures will be chosen with respect to 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 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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