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

From OpenWetWare
Jump to navigationJump to search
Line 16: Line 16:
* Molecules with Arginine bind best to the carboxylate of the amino acids.
* 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.
* 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.




Revision as of 11:15, 6 February 2013

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.



Retrieved from "https://openwetware.org/mediawiki/index.php?title=User:Mary_Mendoza/Notebook/CHEM572_Exp._Biological_Chemistry_II/2013/02/06&oldid=673824"