IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation
Fig 2
IsRNAcirc can significantly reduce the locally irrational topologies contained in initial 3D structures (generated by RNAComposer).
(A-D) Four types of locally irrational topology were identified in initial 3D structures through view inspection: (A) template-free loop due to a lack of related templates in the library, (B) backbone tangle caused by improper template assembly, (C) base collision, in which a backbone segment passes through the middle of two nucleobases, and (D) sharp twist, in which an apparently unreasonable sharp turn is observed in the backbone. The names of circular RNAs for which the relevant irrational topology was observed in the initial 3D structures were also given in top left. (E) The total numbers of locally irrational topologies observed in all initial 3D structures (three structures for each RNA) and the predicted 3D models by IsRNAcirc (five models for each RNA, if available) were displayed in a type-dependent manner. All 34 circular RNAs were considered.