Drug Design: C2N transformation
||Drug Design: C2N transformation
||11/30/2015 - 23:00
||This is the first drug design puzzle!
Can you identify which combinations of atom changes in the binding pocket result in a better binding affinity? Can you do better than medicinal chemists?
Change the atoms around and see if you can get a lower score than the posted score. When the puzzle is completely released, we will show which atoms can be designed and compare those to what medicinal chemists did.
What do you think about the drug design tools? Keep in mind, the tools are a simplified version of the full set of tools. Please report if the puzzle crashes and what you did to make it crash.
Ligand Design Tool:
The Ligand Design tool allows you to add, delete, and modify atoms in a small molecule. For now, we have only allowed the substitution of carbon (C) to nitrogen (N) and vice versa, but many more of the tool’s features will be unlocked as future puzzles are released. In order to modify a small molecule’s atom, all you have to do is click the “Ligand Design” mode, click on the atom of a small molecule that you want to change, and then click on either “C” or “N” to substitute for that atom. It’s a remarkably simple, but powerful tool to utilize in the drug design puzzles.
Ligand View Tool:
This tool works by clicking on it and then the ligand. A series of new viewing options will be available. The hydrogen bond acceptor and donor options allow you to view where the acceptor and donor are on the backbone and sidechain. The repulsive grids show you where you will get a bad score if you have atoms in that location. Finally, the ligand isosurface helps outline the binding pocket.
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