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