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I'm working on a project in biophysics and I need to find if there is a difference in binding of an miRNA to an mRNA when in one case the miRNA is methylated and in the other it isn't. What tools should I use to calculate the binding energy in each case? I have the binding sequence of the miRNA.

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  • $\begingroup$ Something like free energy perturbations? $\endgroup$ – Wise Jan 16 '17 at 6:18
  • $\begingroup$ Yes, after reading about FEP in wikipedia I believe it might be what i'm looking for. $\endgroup$ – Avishai Barnoy Jan 16 '17 at 7:17

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