Dear Rosetta developers,
I am interested in the de novol design of a peptide with helical conformation which could bind a specific protein partner with enhanced affinity. However, when consulting the user guide, i lost my way about the specific method. So could you be so kindly to tell me which method or module in Rosetta can do such kind of case , or provide me a step-by-step guidance.
What i intended to do was listed in the following:
1. Construction of initial models with helical backbone conformations. I hope these models could contact its partners with one helical surface comprised of hydrophobic residues.
2. For each of the models, iterating between sequence optimization and backbone/sidechain refinement for several rounds.
3. Scoring the final models and ranking.
I guess several modules in Resetta may employed simultaneously for above-mentioned steps. Any suggestions will be greatly appreciated.