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single strand DNA in a hairpin conformation

Fri, 02/27/2015 - 14:50 — alliki
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Suggestions and comments

Dear UNRES users,

I was wondering if I could use UNRES somehow in order to solve the DNA folding problem (going from
secondary structure to a three-dimensional model)? I have experimental data and 2D picture of the hairpin conformation.

Thank you in advance for any suggestions

/Urszula

Wed, 03/04/2015 - 11:22 — adam.liwo

Dear Urszula,

We have extended UNRES to nucleic acids (the NARES-2P model; Phys. Rev. Lett., 110, 098101 (2013)). Although it is designed for free simulations, secondary-structure restraints can be imposed as sugar-sugar and/or base-base distance restraints. It is not yet in the UNRES distribution but we can send you this program.

Best,

Adam

UNited RESidue model of proteins (UNRES)