Motif server: web server for undesignable RNA motifs and structures

RNA design aims to find a sequence that can fold into a given (secondary) structure, which has wide applications in science and medicine. However, it has long been known that there are "undesignable structures" for which no sequence can fold into them according to the minimum free energy (MFE) criterion under the standard RNA folding energy model. Our previous work showed that undesignable structures can be effectively and efficiently identified by searching for rival structures. We further showed that there exist "minimal undesignable motifs" within those undesignable structures, where a (structural) motif is a set of consecutive loops and helices within a secondary structure. To better illustrate our theoretical findings, we built a motif server as a user-friendly visualization tool for undesignable RNA structures and motifs, as well as an interactive demo tool where the user can input a new structure and the server will compute and visualize any undesignable motifs within it on the fly. This server maintains a database of undesignable RNA structures and unique minimal undesignable RNA motifs, allowing the users to explore, visualize, analyze, and identify undesignable motifs in existing and new RNA structures. The importance of this server is that it provides a database of motifs for nanostructure design that should not be incorporated because these motifs are unlikely to be achievable. Availability: Our server is at https://linearfold.eecs.oregonstate.edu/motifserver.