[roscoebeezie]

I'm not OP, but what about the realm outside of rational protien design? DNA base paring rules are pretty well understood and we should be able to build useful tools using them. Is there any work out there using only for computation?

[jfarlow]

Yep - and because DNA's base pairing rules are so well-studied, so predictable, and information-carying, we can use DNA for its material properties in addition to or even separate from its genetic properties. In terms of software, Shawn Douglas built CADNano [1] - software to do precisely that. By using DNA as a material it can be useful in its own right - with all sorts of interesting 3D structures, 3D logic, and with atomic precision, built into the encoded base pairs. But these structures generally do not interact with DNA at a genetic level in an organism.

In terms of protein design at that atomic level, the computation traditionally has relied on knowing or guessing at the structure (atomic arrangement) of the protein. And without that, there's not much to do (that's where our work picks up). A lot of that kind of protein design computation work is being done with software like Rosetta [2].

[1] https://cadnano.org/

[2] https://www.rosettacommons.org/