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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.
Project name
