Forgive what may be a naive question (novice Rosetta user here), but I was wondering whether there is a way, using existing Rosetta scripts, to take a primary amino acid sequence and predict the disulfide bonding pattern. To explain a bit better, I am interested in cysteine knot peptides. Many of these have known NMR structures, and if I want to use these in the standard motif grafting -> interface design -> forward fold validation pipeline, I can extract the disulfide bond pattern from those .pdb files for use in forward folding of variants (just instruct the script to keep the same disulfide pattern but relax / fold the rest of it). However, the list of such peptides with known NMR structures is very small when compared to the number of such proteins found in protein sequence databases (i.e. homologs).
Would it be best to rely on homology to peptides with known structures, assigning disulfide patterns that way? Or is there a way to take the primary sequence, and directly predict the disulfide pattern absent any other known structural information, for incorporation in design / relaxation / folding down the road?