Attention all you good coders
Any modified recipes that will help a folded protein to ligands might be useful on the design puzzles for COVID. Bruno Kestemont suggested adapting GAB. I don't know if Brow42's missing ligand would work. I only cook food, so ideas are welcome
Maybe try the recipe BandOntoSphere1.0
https://fold.it/portal/recipe/102961
You first have to make a hub band from
the protein to a point in space that
you want to be the center of a sphere.
For example, you could do show voids
and band to a gap in the ligand/target/
immobile protein that is full of voids.
Then, if your ligand/target/immobile
protein is segments 1-92 while your
designable binder protein is segments
93-152, set BandOntoSphere1.0 to make
bands to just segments 93-152. I
recommend 0 for the band target lengths,
0.1-0.3 for the band strengths, and
setting keep hub to 0 (this will remove
the hub band).
Once BandOntoSphere1.0 has made its
bands, you can run other Recipes that
raise the score while preserving user
supplied bands.
GAB has 2 options: AlwaysUse and UseSegments. They could be of use.
If anyone is interested in adapting one of the
many Rav3n_pl GAB or GAB BiS versions, I have
a bunch of ideas I wish someone would implement.
Please e-mail me if you're interested.
Thanks!
Jeff
I found that GUI compressor worked really well. Since it is a by stride function however it is now broken and will have to wait to see if it will be fixed again. I used GABs now but the distribution of the bands does not seems to work as well.