4 replies [Last post]
Joined: 06/06/2013
Groups: Gargleblasters

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

jeff101's picture
User offline. Last seen 1 hour 26 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Try BandOntoSphere1.0 ?

Maybe try the recipe BandOntoSphere1.0

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.

robgee's picture
User offline. Last seen 18 hours 44 min ago. Offline
Joined: 07/26/2013
GAB options

GAB has 2 options: AlwaysUse and UseSegments. They could be of use.

jeff101's picture
User offline. Last seen 1 hour 26 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Some ideas for future Rav3n_pl GAB or GAB BiS versions:

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.


alcor29's picture
User offline. Last seen 10 hours 47 min ago. Offline
Joined: 11/16/2012
band ligands

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.


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons