I am using the Rosetta software to make comparisons with a peptide folded by a molecular dynamics protocol. Although, I am encountering some issues as, for example, the sheets modelling.
In my molecular dynamics assay I found a b-hairpin-like conformation for the peptide evaluated, but Rosetta only gives me structures featuring alpha-helixes.
I read some discussions pointing to a deficience in Rosetta's algorithm on beta-sheet formation so I wanted to know if there is a practical way of favouring a beta-hairpin conformation without biasing my results.
Thanks, Pedro Torres