ArticleBMC genomics2019
RMalign: an RNA structural alignment tool based on a novel scoring function RMscore.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Machine Learning for RNA-Targeting Drug Design.Journal of chemical information and modeling · 2026Review
- ARTEM server: an online tool for nucleic acid 3D motif searches, 3D structure superposition and structure-based alignment.Nucleic acids research · 2026Article
- Geometric Deep Learning Reveals Ligandable and Cryptic RNA Binding Small Molecule Pockets (SMARTPocket).bioRxiv : the preprint server for biology · 2026Article
- A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align.Nature protocols · 2026Review
- Benchmarking the methods for predicting base pairs in RNA-RNA interactions.Bioinformatics (Oxford, England) · 2025Article
- DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning.Nucleic acids research · 2025Article
- ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment.Nucleic acids research · 2024Article
- A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures.Nucleic acids research · 2023Article
- CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching.Nucleic acids research · 2023Article
- A unified approach to sequential and non-sequential structure alignment of proteins, RNAs, and DNAs.iScience · 2022Article
- US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes.Nature methods · 2022Article
- Dissecting and predicting different types of binding sites in nucleic acids based on structural information.Briefings in bioinformatics · 2022Article
- RR3DD: an RNA global structure-based RNA three-dimensional structural classification database.RNA biology · 2021Article
- Methods for Molecular Modelling of Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2021Review
- LocalSTAR3D: a local stack-based RNA 3D structural alignment tool.Nucleic acids research · 2020Article
- PRIME-3D2D is a 3D2D model to predict binding sites of protein-RNA interaction.Communications biology · 2020Article
- RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA.Bioinformatics (Oxford, England) · 2019Article
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Authors and funding
4 authors.
Funding
Abstract
backgroundRNA-protein 3D complex structure prediction is still challenging. Recently, a template-based approach PRIME is proposed in our team to build RNA-protein 3D complex structure models with a higher success rate than computational docking software. However, scoring function of RNA alignment algorithm SARA in PRIME is size-dependent, which limits its ability to detect templates in some cases.
resultsHerein, we developed a novel RNA 3D structural alignment approach RMalign, which is based on a size-independent scoring function RMscore. The parameter in RMscore is then optimized in randomly selected RNA pairs and phase transition points (from dissimilar to similar) are determined in another randomly selected RNA pairs. In tRNA benchmarking, the precision of RMscore is higher than that of SARAscore (0.88 and 0.78, respectively) with phase transition points. In balance-FSCOR benchmarking, RMalign performed as good as ESA-RNA with a non-normalized score measuring RNA structural similarity. In balance-x-FSCOR benchmarking, RMalign achieves much better than a state-of-the-art RNA 3D structural alignment approach SARA due to a size-independent scoring function. Take the advantage of RMalign, we update our RNA-protein modeling approach PRIME to version 2.0. The PRIME2.0 significantly improves about 10% success rate than PRIME.
conclusionBased on a size-independent scoring function RMscore, a novel RNA 3D structural alignment approach RMalign is developed and integrated into PRIME2.0, which could be useful for the biological community in modeling protein-RNA interaction.
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