User:Dhea Patel/Notebook/CHEM 572: ADA&Inhibitor Kinetics/2013/02/06

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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Project name</span>
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|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
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|colspan="2" style="background-color: #F2F2F2;" align="right"|[[{{FULLPAGENAME}}/Entry_Base|Customize your entry pages]] [[Help:Notebook/Project_Base/Customize_entry_page|<html><img src="/images/a/aa/Help.png" border="0" /></html>]]
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==Entry title==
 
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* Insert content here...
 
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taken from [[User:Mary_Mendoza/Notebook/CHEM572_Exp._Biological_Chemistry_II/2013/02/06|Mary's Notebook]]. We performed all the following steps together.
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==Screening==
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* 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.
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* Opened Maestro and imported the docked structures from last week.
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* Structures were sorted by docking score
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* The molecules were chosen based on two criteria, (1) similarity with aspirin and (2) basis of docking score.
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* The similarity of compounds to aspiring is indicated by the Tanimoto coefficient.
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* On the workspace, observed the structures with its bonding to the amino acids located on the binding pocket.
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* Molecules with Arginine bind best to the carboxylate of the amino acids.
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* Some molecules are efficient in terms of geometry and size but exhibit few hydrogen bonds.
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* Under the property options > show all
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* Select the fpscreen_01-1, sorted by the Tanimoto coefficient.
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* 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.
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* 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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* After selecting the molecules, the structures were viewed under 2D Sketcher.
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* The zinc ID number for each structure were entered to the zinc website to verify its availability for purchase.
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* The table of structures were exported to excel to view the vendor list.
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* Eight structures were chosen based on their docking score and five for their similarity to aspirin.
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* The final list of structures were uploaded into dropbox and posted below.
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[[Image:Struc1.png|center]]
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[[Image:Orderlist.png]]
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Revision as of 14:13, 13 February 2013

Search this Project

Customize your entry pages

taken from Mary's Notebook. We performed all the following steps together.

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.


Image:Orderlist.png


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