design puzzle : avoid collision with protein where the target protein is sticked
|Opened on:||Sunday, July 5, 2020 - 13:16|
|Last modified:||Monday, July 6, 2020 - 17:26|
In design puzzle, we create a protein that have hydrogen bouds with a zone of a target protein.
This target is often stick with an other protein in real life, and we have to make sure there is no collision on it with our protein.
There is a zone that have movable sidechains in the target, it helps us to know were we have to create bouds. But it is not enough.
We can have collisions with the other sticked proteins, and we can't know that in game.
It can be interesting in some designs to have contact with target protein, not only in the movable sidechain zone, but a little around.
Because we need something that stay stick, and sometimes a part of the shape around can be used.
It can be usefull to avoid mistake too. This is already hapened with hight score proteins.
To resolve this : We can just add a zone that represent a part of the protein where the target is sticked, or just add a zone that make clashs if our protein go on it.