Table 1.
Benchmark test results for 3D structure prediction by IsRNA1, SimRNA, and iFoldRNA for 130 relatively large RNAs (40-161 nts) with native 2D structures as constraints. Average/median (in boldface) structural quality assessments in terms of RMSD, INFall, and clash score are shown. The results are classified according to the structural topologies for the top-1 prediction and the best of the top-3 predictions (if available). The numbers of the test cases are given in parentheses. The prediction results for iFoldRNA and SimRNA were collected from iFoldRNAv2 webserver (https://dokhlab.med.psu.edu/ifoldrna/#/) and SimRNA program provided by authors (https://ftp.users.genesilico.pl/software/simrna/) using default parameters, respectively. RMSDs were calculated over all-heavy atoms. INFall is the Interaction Network Fidelity for all the canonical and non-canonical base-pairing and base-stacking interactions.
| Dataset and folding model | Top 1 prediction | Best of top 3 predictions | ||||
|---|---|---|---|---|---|---|
| RMSD (Å) | INFall | Clash Score | RMSD (Å) | INFall | Clash Score | |
| Stem-loop | ||||||
| IsRNA1 (44) | 5.79/5.08 | 0.80/0.82 | 2.0/1.4 | 5.15/4.57 | 0.81/0.82 | 1.8/1.3 |
| SimRNA (44) | 7.21/5.49 | 0.77/0.79 | 129.4/128.5 | 6.58/5.06 | 0.77/0.79 | 128.5/128.3 |
| iFoldRNA (32) | 7.90/5.57 | 0.70/0.73 | 153.2/143.1 | 7.29/5.17 | 0.71/0.73 | 151.4/143.1 |
| Multi-way junction | ||||||
| IsRNA1 (43) | 12.93/11.33 | 0.71/0.73 | 4.2/2.9 | 10.88/10.6 | 0.72/0.73 | 4.7/2.8 |
| SimRNA (43) | 14.91/13.36 | 0.69/0.69 | 143.3/144.4 | 12.42/11.48 | 0.69/0.70 | 143.7/144.4 |
| iFoldRNA (34) | 15.85/14.57 | 0.64/0.65 | 180.7/181.0 | 13.98/12.74 | 0.64/0.64 | 183.7/183.8 |
| Tertiary interaction | ||||||
| IsRNA1 (43) | 9.89/8.16 | 0.74/0.73 | 5.7/4.8 | 9.05/7.62 | 0.75/0.75 | 5.7/4.8 |
| SimRNA (43) | 11.75/10.91 | 0.73/0.73 | 146.5/150.7 | 10.28/8.94 | 0.71/0.72 | 147.9/144.9 |
| iFoldRNA (29) | 11.60/11.76 | 0.67/0.69 | 177.4/178.9 | 11.22/11.48 | 0.66/0.68 | 175.2/180.0 |
| All | ||||||
| IsRNA1 (130) | 9.51/8.12 | 0.75/0.75 | 4.0/2.7 | 8.34/7.13 | 0.76/0.76 | 4.07/2.45 |
| SimRNA (130) | 11.26/10.95 | 0.73/0.73 | 139.7/140.0 | 9.73/8.92 | 0.72/0.73 | 139.9/139.6 |
| iFoldRNA (95) | 11.87/11.37 | 0.67/0.68 | 170.4/174.6 | 10.88/10.46 | 0.67/0.68 | 170.2/173.1 |
| Multiple chains | ||||||
| IsRNA1 (35) | 8.72/7.93 | 0.78/0.79 | 3.4/2.3 | 7.78/6.24 | 0.79/0.79 | 3.5/2.4 |
| SimRNA (35) | 12.10/12.91 | 0.77/0.76 | 137.7/136.7 | 10.22/9.60 | 0.77/0.77 | 138.4/137.8 |