PlanarFold: a coarse-grained molecular dynamics model of RNA in two-dimensional space (opens in new tab)

RNAs serve versatile functional roles by virtue of their structures and dynamics. RNA computational models are typically tailored to either perform structural modeling or solve a specific class of folding problems. Here, we present PlanarFold, a coarse-grained RNA model that integrates molecular dynamics simulation in two-dimensional space with dynamic programming to explore the diverse dynamic behaviours of RNAs, achieving a speedup of more than four orders of magnitude compared with all-ato...