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I am trying to design an orthogonal ligand/receptor system. I've inherited the script below as a starting point but I'm wondering what exactly the Docking mover would be doing. My PDB structure is a ligand that is already bound to the binding domains on the receptor. Does it still make sense to perform a docking step in this scenario?
I am trying to use MotifGraft mover to graft an epitope to a scaffold protein (actually there is a structure library, parsed with -l list).
The xml script is attached.
My command line is as follow (I am first trying a very loose boundary conditions, I'm aware about the higher RMSD/atom_clash values):
I'm trying to to use rosetta design (http://rosettadesign.med.unc.edu) to increase binding affinity between 2 proteins in 1 pdb file.
I want 2 residue ranges to be mutated in chain B but all other residues to remain the same. Therefore I have used this resfile:
71 - 88 B ALLAAxc EX1
50 - 56 B ALLAAxc EX1
However, the server mutates residues in both chains. How do I force it to only mutate chain B?
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