Fig 1.
Benchmark data.
Fig 2.
Types of entanglements of structure elements.
Elements include loops (L), dinucleotide steps (D), or single strands (S). Intersection points are depicted as red balls.
Fig 3.
Disentanglement process: (1) RNAspider-to-SPQR data reformatting and reduction of loops around intersection points; (2) SPQR simulations that pull apart the fragments involved in the entanglement; (3) All-atom refinement.
Table 1.
Statistics on entanglements in the analyzed datasets.
Table 2.
Statistics on evaluation measures for RNA models with at least one resolved entanglement (108 cases).
Fig 4.
Example interlaces in the dataset: D&D in R1126TS110_1 – (A) linked and (B) resolved; D&L in PZ28_Bujnicki_4 – (C) linked and (D) resolved; L&L in PZ24_Kollmann_3 – (E) reduced and linked, (F) reduced and resolved.
Fig 5.
Reduction and removal of the R1138TS076_3 interlace L&L, (A) unreduced, (B) reduced and (C) reduced and untangled. For L(S) lasso from the R1107TS054_3 model: (D) unreduced, (E) reduced, (F) reduced and untangled.
Fig 6.
Example lassos in CASP15 models: D(D) in R1116TS470_1 – (A) entangled and (B) resolved; D(L) in R1136TS110_4 – (C) linked and (D) resolved; D(S) in R1138TS185_4 – (E) entangled and (F) resolved.