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

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==Computational 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.


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Revision as of 15:14, 8 May 2013

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