Charge spheres for sidechains

Started by tjohnson

tjohnson Lv 1

Please consider having a view that looks solely at the electrical properties of the objects (backbones and sidechains).
I suggest that there be a way to visualize the charges of the sidechains and backbones the way that voids are represented.
I think a feature like this could be very useful to understanding how things fit together. If for instance one could see that a given object is minus 1 or 2 electrons and one could see another object has 1 electron available like the stick and ball models then I think this may facilitate the building of better solutions.

In order to make it both useful and intutitive I think one may want to use colors and have those colors shift when two objects get close enough like red and blue make purple or yellow and blue make green. I suggest that the actual value information be available with a mouse over or an onscreen legend, in addition to the color combining method of visualizing. I don't know if this would be too resource intensive to implement, but I wanted to share my thoughts on this.

Thanks,
Tim

axcho Lv 1

I don't know much about the chemical properties of these proteins. Is electrical charge particularly important?

I do know that the current scoring function doesn't even take into account positive/negativeness of sidechains, even though that can sometimes affect the way hydrophilic (polar) sidechains interact.

Brad Taylor Lv 1

Even if it's not in the score, doesn't sidechain charge have to be taken into account in the energy function?
In any case. I would appreciate being able to see both red and blue hydrophilic sidechains, even if just to be able to distinguish between Glutamine and Glutamate.

Do you think sidechain charge is intentionally being hidden from us to prove the point that it's not important in directed folding?

Seth Cooper Staff Lv 1

I'm working on a CPK colored ball and stick model, which gives a better picture of the individual atoms and their properties. It may make it into the game in some form!