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 Saccharomyces cerevisiae tRNAs and 5S rRNAs and found that suboptimal secondary structures obtained after the simulations include accurate structures.
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| Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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| Site | Modification | Modifier | Source | Reference |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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| Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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| Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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| Evidence ID | Analyze ID | File | Description |
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