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Assume there's a short sequence of an amino acids.
I am using molecular structuring softwares to look at secondary structure. But it's blackbox method. In plain theory, how to determine what structure the above peptide will fold into? There must be a basic set of rules, prior to all the complex maths, and modelling?
Based on basic rules I also want to know what and how a different amino acid contributes to the formation specificity. Will add more details.