Motivation RNA design is the search for a sequence or set of sequences that will fold to
desired structure, also known as the inverse problem of RNA folding. However, the
sequences designed by existing algorithms often suffer from low ensemble stability, which
worsens for long sequence design. Additionally, for many methods only a small number of
sequences satisfying the MFE criterion can be found by each run of design. These
drawbacks limit their use cases. Results We propose an innovative optimization paradigm …