Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model.

ABSTRACT: Noncanonical base pairs contribute crucially to the three-dimensional architecture of large RNA molecules; however, how to accurately model them remains an open challenge in RNA 3D structure prediction. Here, we report a promising coarse-grained (CG) IsRNA2 model to predict noncanonical base pairs in large RNAs through molecular dynamics simulations. By introducing a five-bead per nucleotide CG representation to reserve the three interacting edges of nucleobases, IsRNA2 accurately models various base-pairing interactions, including both canonical and noncanonical base pairs. A benchmark test indicated that IsRNA2 achieves a comparable performance to the atomic model in de novo modeling of noncanonical RNA structures. In addition, IsRNA2 was able to refine the 3D structure prediction

SUBMITTER: Zhang D 

PROVIDER: S-EPMC9731381 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature