fixing sequence during grafting in antibody_designer

[Anonymous]

Using antibody_designer to graft loops on one CDR. I’d like to fix the sequence of the grafted loop to native. It appears to ignore the 

I have tried something like this in my cdr_instruction file

H3 GraftDesign ALLOW

ALL SeqDesign FIX

 I’ve also tried passing it a resfile forcing everything to be native like so

NATAA

start

But, it does not seem to follow this. Does NATAA in the context of grafting mean that use native sequence of cdr being grafted? Or, is NATAA just being ignored in the context of grafting? 

I’ve even tried manually listing out the positions that will be grafted in the resfile and explicitly giving the desired AA identity. This throws an error saying one of the positions I specified was not in the pdb even though it is in the input pdb. Is there some renumbering going on here during grafting?  I did renumber the pdb to the AHo scheme before running antibody_designer. Also, I am keeping the loops the same length as native, so I would not expect renumbering.

[Anonymous]

When you graft in a CDR, the sequence comes with the graft.  So SeqDesign FIX means that AFTER grafting, no sequence design is done. Are you grafting the same cluster?  The minimization of the loops use constraints that are built from the current cluster – so grafting in the same cluster and using the sequence from your native is not going to do much. 

 The RESFILE should work to design the sequence back on.   Can you post your inputs so that I may debug it?  Yes, NATAA means that it will not design the <grafted> CDR.  You will need to put the positions and the PIKAA of the exact sequence you started with. 

You can also call RAbD in RosettaScripts – so you could use the SimpleThreadingMover after each call to RAbD – https://www.rosettacommons.org/docs/wiki/scripting_documentation/RosettaScripts/Movers/movers_pages/SimpleThreadingMover

https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/Movers-RosettaScripts#meta-movers

 

The other way you could do this is to us constraints or score terms to favor native sequence:  This may work: https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/FavorNativeResidueMover

https://www.rosettacommons.org/docs/wiki/rosetta_basics/scoring/design-guidance-terms

 

-Jared

[Author]

Posts