ddG_RNA final energy different when modeling WT sequence

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    • January 25, 2022 at 10:41 pm #3903
      Anonymous

        Hi, I have been using the ddG_RNA tool within ROSIE to calculate relative affinities for my protein and a list of mutant RNAs. Included in the text file list is the WT sequence that is also specified in the PDB file. Based on how I understand the tool works, the ddG bind score for this RNA should be 0, since the value is relative to the WT sequence. Instead I get a score of 3.36. Any idea on why this would be happening? 

        I am using RNAfold to calculate the mfes for the list of mutant sequences, is it possible that I need to set different folding parameters?

        Thank you,

        Alex

         

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