Unafold's calculations run fine with the currently installed version, but it can produce 2D plots of the structures it calculates. Therefore it needs mfold_utils (part of the predecessor of UNAFold), which is described at http://mfold.rna.albany.edu/?q=mfold/download-mfold.
For the full functionality of UNAFold it would be necessary to create a (very simple) ebuild for mfold_utils and introduce a USE flag for UNAFold which pulls in mfold_utils.
Local tests on my amd64 machine worked quite fine, mfold_utils compiles with some QA warnings, but is functional and provides the needed binaries to UNAFold.
Created attachment 450366 [details, diff]
diff to the current in-tree unafold ebuild
I just added the required capability, but it will need a new ebuild (this bug depends on bug #597242).
Both ebuilds are available in my overlay: https://github.com/thinrope/pkalin