3D feasibility of 2D RNA-RNA interaction paths by stepwise folding simulations.

ABSTRACT: The structure of an RNA, and even more so its interactions with other RNAs, provide valuable information about its function. Secondary structure-based tools for RNA-RNA interaction predictions provide a quick way to identify possible interaction targets and structures. However, these tools ignore the effect of steric hindrance on the tertiary (3D) structure level, and do not consider whether a suitable folding pathway exists to form the interaction. As a consequence, these tools often predict interactions that are unrealistically long and could be formed (in three dimensions) only by going through highly entangled intermediates. Here, we present a computational pipeline to assess whether a proposed secondary (2D) structure interaction is sterically feasible and reachable along a plausible

SUBMITTER: Beckmann IK 

PROVIDER: S-EPMC10798244 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature