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

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==Entry title==
taken from [[User:Mary_Mendoza/Notebook/CHEM572_Exp._Biological_Chemistry_II/2013/02/06|Mary's Notebook]]. We performed all the following steps together.
* Insert content here...


==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:Struc1.png|center]]
[[Image:Orderlist.png]]


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Revision as of 10:31, 8 February 2013

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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.



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