Hello, I am new at protein modelling, I used I-tasser to predict structure of a set (280) cysteine rich peptides (plant defensins) and the disulfide bonds formed were completely off. up to the point when 3 cysteines bonded together in some structures. I have used restrains to specify CONTACT between cysteines, but not the distance. The models have a good C-score, according to your manual.
Is there any way to precalculate the distance and give it to the program?
Should it just be the length of the disulfide bond ?
Is there any other way to force pairing of cysteines in the structure?
Also is there a way to extract secondary structure only from I-tasser?
thank you in advance,
Srdjan