Tue, 11/20/2012 - 04:30
#2
Not realistic at all!
The filter will not allow me to place hydrophobes anywhere on a helix. I want to place hydrophobes in the area between two helices (the "inside"), while keeping the area to the outside of both hydrophilic. But no matter where I try to mutate a helix, it never lets me choose a hydrophobic, because all parts of a helix are apparently "outside".
I don't want to mutate my protein before I place it in some type of organized structure(s).
Am I doing something wrong, here? I am hearing cries like mine throughout chat. I really think the devs ned to re-consider how this filter works, or even if it we need it.
How about scoring "proper" sidechains better, but allowing us to mutate to whatever we think best?
For more info on the Layer Design filter, please see: http://fold.it/portal/node/993855