RNA folding pathways from all-atom simulations with a variationally improved history-dependent bias.

ABSTRACT: Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. As a step forward in tackling these issues, we extend to RNA an enhanced path-sampling method previously successfully applied to proteins. In this scheme, the information about the RNA's native structure is harnessed by a soft history-dependent biasing force promoting the generation of productive folding trajectories in an all-atom force field with explicit solvent. A rigorous variational principle is then applied to minimize the effect of the bias. Here, we report on an application of this method to RNA molecules from 20 to 47 nucleotides long and increasing topol

SUBMITTER: Lazzeri G 

PROVIDER: S-EPMC10432211 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature