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

From OpenWetWare
< User:Mary Mendoza‎ | Notebook‎ | CHEM572 Exp. Biological Chemistry II‎ | 2013‎ | 02
Revision as of 13:02, 6 February 2013 by Mary Mendoza (talk | contribs) (Computational Screening)
Jump to: navigation, search
Owwnotebook icon.png Project name <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>

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.