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

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Computational Screening)
(Computational Screening)
Line 22: Line 22:
* Some molecules have high docking scores but do not have affinity to the binding pocket. Thus, docking scores are unreliable for this circumstance.  
* 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.

Revision as of 14:15, 6 February 2013

Project name Main project page
Previous entry      Next entry

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.



Personal tools