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Chen X, Zhang S. CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching. Nucleic Acids Res 2023; 51:e53. [PMID: 36987885 PMCID: PMC10201423 DOI: 10.1093/nar/gkad222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 03/04/2023] [Accepted: 03/28/2023] [Indexed: 03/30/2023] Open
Abstract
The functions of non-coding RNAs usually depend on their 3D structures. Therefore, comparing RNA 3D structures is critical in analyzing their functions. We noticed an interesting phenomenon that two non-coding RNAs may share similar substructures when rotating their sequence order. To the best of our knowledge, no existing RNA 3D structural alignment tools can detect this type of matching. In this article, we defined the RNA 3D structure circular matching problem and developed a software tool named CircularSTAR3D to solve this problem. CircularSTAR3D first uses the conserved stacks (consecutive base pairs with similar 3D structures) in the input RNAs to identify the circular matched internal loops and multiloops. Then it performs a local extension iteratively to obtain the whole circular matched substructures. The computational experiments conducted on a non-redundant RNA structure dataset show that circular matching is ubiquitous. Furthermore, we demonstrated the utility of CircularSTAR3D by detecting the conserved substructures missed by regular alignment tools, including structural motifs and conserved structures between riboswitches and ribozymes from different classes. We anticipate CircularSTAR3D to be a valuable supplement to the existing RNA 3D structural analysis techniques.
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Affiliation(s)
- Xiaoli Chen
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
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Zhang C, Shine M, Pyle AM, Zhang Y. US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nat Methods 2022; 19:1109-1115. [PMID: 36038728 DOI: 10.1038/s41592-022-01585-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022]
Abstract
Structure comparison and alignment are of fundamental importance in structural biology studies. We developed the first universal platform, US-align, to uniformly align monomer and complex structures of different macromolecules-proteins, RNAs and DNAs. The pipeline is built on a uniform TM-score objective function coupled with a heuristic alignment searching algorithm. Large-scale benchmarks demonstrated consistent advantages of US-align over state-of-the-art methods in pairwise and multiple structure alignments of different molecules. Detailed analyses showed that the main advantage of US-align lies in the extensive optimization of the unified objective function powered by efficient heuristic search iterations, which substantially improve the accuracy and speed of the structural alignment process. Meanwhile, the universal protocol fusing different molecular and structural types helps facilitate the heterogeneous oligomer structure comparison and template-based protein-protein and protein-RNA/DNA docking.
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Affiliation(s)
- Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Morgan Shine
- Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA
| | - Anna Marie Pyle
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA.,Department of Chemistry, Yale University, New Haven, CT, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA. .,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
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Chen X, Khan NS, Zhang S. LocalSTAR3D: a local stack-based RNA 3D structural alignment tool. Nucleic Acids Res 2020; 48:e77. [PMID: 32496533 PMCID: PMC7367197 DOI: 10.1093/nar/gkaa453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/15/2020] [Accepted: 05/27/2020] [Indexed: 11/29/2022] Open
Abstract
A fast-growing number of non-coding RNA structures have been resolved and deposited in Protein Data Bank (PDB). In contrast to the wide range of global alignment and motif search tools, there is still a lack of local alignment tools. Among all the global alignment tools for RNA 3D structures, STAR3D has become a valuable tool for its unprecedented speed and accuracy. STAR3D compares the 3D structures of RNA molecules using consecutive base-pairs (stacks) as anchors and generates an optimal global alignment. In this article, we developed a local RNA 3D structural alignment tool, named LocalSTAR3D, which was extended from STAR3D and designed to report multiple local alignments between two RNAs. The benchmarking results show that LocalSTAR3D has better accuracy and coverage than other local alignment tools. Furthermore, the utility of this tool has been demonstrated by rediscovering kink-turn motif instances, conserved domains in group II intron RNAs, and the tRNA mimicry of IRES RNAs.
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Affiliation(s)
- Xiaoli Chen
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Nabila Shahnaz Khan
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
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Gong S, Zhang C, Zhang Y. RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA. Bioinformatics 2020; 35:4459-4461. [PMID: 31161212 DOI: 10.1093/bioinformatics/btz282] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/17/2019] [Accepted: 04/18/2019] [Indexed: 11/13/2022] Open
Abstract
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.
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Affiliation(s)
- Sha Gong
- School of Physics and Electronic Information, Huanggang Normal University, Huanggang, China.,Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
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Zheng J, Xie J, Hong X, Liu S. RMalign: an RNA structural alignment tool based on a novel scoring function RMscore. BMC Genomics 2019; 20:276. [PMID: 30961545 PMCID: PMC6454663 DOI: 10.1186/s12864-019-5631-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 03/20/2019] [Indexed: 01/30/2023] Open
Abstract
Background RNA-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. Results Herein, 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. Conclusion Based 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. Electronic supplementary material The online version of this article (10.1186/s12864-019-5631-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinfang Zheng
- School of Physics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Juan Xie
- School of Physics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Xu Hong
- School of Physics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Shiyong Liu
- School of Physics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
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Islam S, Ge P, Zhang S. CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures. Nucleic Acids Res 2017. [PMID: 28641399 PMCID: PMC5737500 DOI: 10.1093/nar/gkx538] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The analysis of RNA tertiary structure is hindered by the fact that not too many structural data are available and a significant amount of them are in low resolution. Due to the atomic coordinate errors posed by the limitations of low-resolution RNA three-dimensional structures, it becomes a critical challenge to extract key geometric characteristics of RNA, particularly, the interaction of bases. To address this issue, we have devised a comparative method, named CompAnnotate, that utilizes more precise structural information of high-resolution homologs to annotate the base-pairing interactions in the low-resolution structures, by aligning and making comparative geometric assessments. The benchmarking results show that our method can improve the annotations of the existing methods significantly. We have achieved different levels of improvements for various methods and datasets, including an example of significant sensitivity and precision enhancement from 28 to 57% and from 53 to 82%, respectively.
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Affiliation(s)
- Shahidul Islam
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Ping Ge
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
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Holzhauser E, Ge P, Zhang S. WebSTAR3D: a web server for RNA 3D structural alignment. Bioinformatics 2016; 32:3673-3675. [DOI: 10.1093/bioinformatics/btw502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/17/2016] [Accepted: 07/26/2016] [Indexed: 11/13/2022] Open
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