ArticleNAR genomics and bioinformatics2025
StraD: a coarse-grained simulation of co-transcriptional RNA folding.
Article in NAR genomics and bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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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 folding simulations of artificial RNA switches. We found that the simulation results for the artificial RNA switches reproduced those by a fine-grained simulation method, Kinfold. Moreover, with Kinfold and StraD, we performed co-transcriptional folding simulation of
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