Predicted stable RNA folds

70 predicted stable RNA folds

(Manfredonia 2020 doi: 10.1101/2020.06.15.151647) in vitro SHAPE

• by using the SimRNA method (Boniecki et al., 2015), we modeled their 3D folding
• generated 1000 lowest-energy models to represent the most stable 3D conformations.
• secondary structures agreed very well with that inferred from experimental probing, the 3D structures exhibited significant overall conformational variability, which was expected given the elongated character of secondary structures inferred from experimental data. Nonetheless, the 3D modeling revealed a number of persistent complex spatial motifs, often comprising junctions and structured bulges and loops.
• Fpocket software (Guilloux et al., 2009) to score the putative druggable sites in 1000 lowest-energy models for each RNA segment
• The majority of targetable pockets are found in high-information-content structures such as multiway junctions
• which of the 149 sites are most conserved or do co-variate: 12 sites

selected druggable domains

(Manfredonia 2020 doi: 10.1101/2020.06.15.151647) in vitro SHAPE

• s2m, segment 29548-29870; Figure S57
• FSE , segment 13367-13546; Figure S27
• SL5 element of Sarbecovirus 5′ UTR and the 3′ UTR (Figure S60)

prediction of RNA folds

PMID: 36389431 - validation with SHAPE-map of CoV2 data