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Assume there's a short sequence of an amino acids.

MAKMGSKKKAGHGGKEKLENMGE

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.

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marked as duplicate by Bryan Krause, David, another 'Homo sapien', James, Satwik Pasani Jul 5 '17 at 10:20

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  • $\begingroup$ @BryanKrause that's helpful. But what I really want to know why? Like what bonds, interactions of these amino acids contributes to the specificity of forming helix or beta etc. How it is so. I will update my answer. Cheers. $\endgroup$ – bonCodigo Jul 1 '17 at 0:53
  • $\begingroup$ @benCodigo A lot of that would just be on the wiki pages for those types of structures. eg: en.wikipedia.org/wiki/Alpha_helix#Structure $\endgroup$ – Bryan Krause Jul 1 '17 at 1:26
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    $\begingroup$ Afaik there are no excat rules for this. The methods are based on (known) statistics of the presence / absence of certain amino acids in helices and beta-sheets (e.g. proline and glycine almost never occur in helices) $\endgroup$ – Nicolai Jul 1 '17 at 4:38