Towards Automated Design of Riboswitches
Frederic Runge Jörg K. H. Franke Frank Hutter
Experimental screening and selection pipelines for the discovery of novel
riboswitches are expensive, time-consuming, and inefficient. Using
computational methods to reduce the number of candidates for the screen could
drastically decrease these costs. However, existing computational approaches do
not fully satisfy all requirements for the design of such initial screening
libraries. In this work, we present a new method, libLEARNA, capable of
providing RNA focus libraries of diverse variable-length qualified candidates.
Our novel structure-based design approach considers global properties as well
as desired sequence and structure features. We demonstrate the benefits of our
method by designing theophylline riboswitch libraries, following a previously
published protocol, and yielding 30% more unique high-quality candidates.