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

(Difference between revisions)

Revision as of 16:09, 6 February 2013

Project name

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.

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.

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-==Computational Screening==
+==Screening==
 * Maestro imported structures
 * Structures were sorted by docking score
@@ Line 17: / Line 17: @@
 * 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.