RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA
By Sha Gong, Chengxin Zhang, Yang Zhang. 2019
86 citations recorded by the source corpus.
MOTIVATION Comparison of RNA 3D structures can be used to infer functional relationship of RNA molecules. Most of the current RNA structure alignment programs are built on size-dependent scales, which complicate the interpretation of structure and functional relations. Meanwhile, the low speed prevents the programs from being applied to large-scale RNA structural database search. RESULTS We developed an open-source algorithm, RNA-align, for RNA 3D structure alignment which has the structure similarity scaled by a size-independent and statistically interpretable scoring metric. Large-scale benchmark tests show that RNA-align significantly outperforms other state-of-the-art programs in both alignment accuracy and running speed. The major advantage of RNA-align lies at the quick convergence of the heuristic alignment iterations and the coarse-grained secondary structure assignment, both of which are crucial to the speed and accuracy of RNA structure alignments. AVAILABILITY AND IMPLEMENTATION https://zhanglab.ccmb.med.umich.edu/RNA-align/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Subfields: Molecular Biology
How researchers see this paper
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In Molecular Biology
- Andriy Kryshtafovych
- Torsten Schwede
- Krzysztof Fidelis
- Yang Zhang
- John Moult
- Rhiju Das
- R. Rangan
- Bohdan Monastyrskyy
Citations in the corpus
- Assessment of three-dimensional RNA structure prediction in CASP15 (2023, positive): “28 The assessment also considered the coordinate comparison metric TM-score as computed in RNA-Align 29 and the Mean of Circular Quanti-ties 30 to assess accuracy in the torsion angle space.”
- Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction (2022, unknown): “2C, we further list the results for the TM-score, an index that is more sensitive to the global fold of the RNA structures 22 .”
- New prediction categories in CASP15 (2023, methodology): “Evaluation measures include Clashscore, 15 Root Mean Square Deviation (RMSD), 16 Local Distance Difference Test (lDDT), 17 Template Modeling score (TM-score), 18 and Global Distance Test-Total Score (GDT-TS).”