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

From OpenWetWare
Jump to: navigation, search
(Computational Screening)
(Screening)
(3 intermediate revisions by the same user not shown)
Line 6: Line 6:
 
| colspan="2"|
 
| colspan="2"|
 
<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
 
<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
==Computational Screening==
+
==Screening==
* Maestro imported structures
+
* The objective of screening compounds for this laboratory period is to obtain a list of compounds that would be ordered and investigated for this project.
 +
* Opened Maestro and imported the docked structures from last week.
 
* Structures were sorted by docking score
 
* Structures were sorted by docking score
* Choose molecules with two criteria similarity with aspirin and basis of docking score.
+
* The molecules were chosen based on two criteria, (1) similarity with aspirin and (2) basis of docking score.
* The structures will be chosen with respect to the Tanimoto coefficient.
+
* The similarity of compounds to aspiring is indicated by the Tanimoto coefficient.
  
  
 
* On the workspace, observed the structures with its bonding to the amino acids located on the binding pocket.
 
* 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.
 
* 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 exhibit few hydrogen bonds.
  
 
* Under the property options > show all
 
* Under the property options > show all
Line 28: Line 29:
 
* The table of structures were exported to excel to view the vendor list.
 
* 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.  
 
* 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 and posted below.
  
 +
[[Image:Struc1.png|center]]
 +
 +
 +
[[Image:Orderlist.png]]
  
 
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->
 
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->

Revision as of 07:55, 8 February 2013

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>

Screening

  • The objective of screening compounds for this laboratory period is to obtain a list of compounds that would be ordered and investigated for this project.
  • Opened Maestro and imported the docked structures from last week.
  • Structures were sorted by docking score
  • The molecules were chosen based on two criteria, (1) similarity with aspirin and (2) basis of docking score.
  • The similarity of compounds to aspiring is indicated by 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 exhibit 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 and posted below.
Struc1.png


Orderlist.png