This paper by former collegues of mine should answer your questions

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002829

Thank you Jessen

Hello Sanjeev Kumar Bhure

There is nothing as different secondary structures having different affinities towards B cell receptors, in particular. What ultimately matters is the outermost conformations that are available during the docking of your molecules with the B cell receptor. Hence it is the surface availability of that epitope sequence that matters, not the secondary structure.

For further information, you can refer to this paper:

Article Structural analysis of B-cell epitopes in antibody: Protein complexes

Hope it Helps.