StraD: a coarse-grained simulation of co-transcriptional RNA folding.

ABSTRACT: Co-transcriptional folding is a fundamental process in living cells. Since transient RNA structures that appear during transcription have crucial functions like molecular recognition in riboswitches, elucidating the mechanism of co-transcriptional folding is an important issue to comprehend RNA functions. In the present paper, we propose a novel algorithm, StraD, for RNA secondary structure kinetics simulation on a coarse-grained energy landscape. StraD explores an energy landscape where secondary structures are enumerated based on a constrained local flooding algorithm. The constraint and local search approach effectively reduces the number of conformations in the enumeration process, enabling StraD to perform efficient flooding-based simulations. We applied StraD to co-transcriptional fo

SUBMITTER: Taneda A 

PROVIDER: S-EPMC12634414 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature