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

(Difference between revisions)

Revision as of 14:15, 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.

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 * 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.