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How to benchmark RNA secondary structure prediction accuracy.如何评估 RNA 二级结构预测准确性。
Methods. 2019 Jun 1;162-163:60-67. doi: 10.1016/j.ymeth.2019.04.003. Epub 2019 Apr 2.
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Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.基于能量的多序列比对中RNA共有二级结构预测
Methods Mol Biol. 2014;1097:125-41. doi: 10.1007/978-1-62703-709-9_7.
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Computational analysis of RNA structures with chemical probing data.利用化学探针数据对RNA结构进行计算分析。
Methods. 2015 Jun;79-80:60-6. doi: 10.1016/j.ymeth.2015.02.003. Epub 2015 Feb 14.
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iFoldRNA v2: folding RNA with constraints.iFoldRNA v2：带约束条件的RNA折叠
Bioinformatics. 2015 Sep 1;31(17):2891-3. doi: 10.1093/bioinformatics/btv221. Epub 2015 Apr 24.
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SARNA-Predict: accuracy improvement of RNA secondary structure prediction using permutation-based simulated annealing.SARNA-Predict：基于排列模拟退火的 RNA 二级结构预测准确性改进。
IEEE/ACM Trans Comput Biol Bioinform. 2010 Oct-Dec;7(4):727-40. doi: 10.1109/TCBB.2008.97.
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SCFGs in RNA secondary structure prediction RNA secondary structure prediction: a hands-on approach.RNA二级结构预测中的SCFGs：RNA二级结构预测：一种实践方法。
Methods Mol Biol. 2014;1097:143-62. doi: 10.1007/978-1-62703-709-9_8.
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RNA Secondary Structure Prediction with Pseudoknots Using Chemical Reaction Optimization Algorithm.基于化学反应优化算法的含假结RNA二级结构预测
IEEE/ACM Trans Comput Biol Bioinform. 2021 May-Jun;18(3):1195-1207. doi: 10.1109/TCBB.2019.2936570. Epub 2021 Jun 3.
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The BRaliBase dent-a tale of benchmark design and interpretation.BRaliBase牙的故事——基准设计与解读
Brief Bioinform. 2017 Mar 1;18(2):306-311. doi: 10.1093/bib/bbw022.
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Sequence Design Using RNAstructure.使用 RNAstructure 进行序列设计。
Methods Mol Biol. 2025;2847:17-31. doi: 10.1007/978-1-0716-4079-1_2.
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Predicting pseudoknotted structures across two RNA sequences.预测两条 RNA 序列中的假结结构。
Bioinformatics. 2012 Dec 1;28(23):3058-65. doi: 10.1093/bioinformatics/bts575. Epub 2012 Oct 8.
引用本文的文献
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ECSFinder: optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences.ECSFinder：从基因组序列中对进化保守RNA二级结构进行优化预测。
Nucleic Acids Res. 2025 Aug 11;53(15). doi: 10.1093/nar/gkaf780.
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AlignmentFold and AlignmentPartition: Improving the align-then-fold approach for RNA secondary structure prediction.比对折叠与比对划分：改进用于RNA二级结构预测的先比对后折叠方法
bioRxiv. 2025 Jul 28:2025.07.23.666478. doi: 10.1101/2025.07.23.666478.
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RiNALMo: general-purpose RNA language models can generalize well on structure prediction tasks.RiNALMo：通用RNA语言模型在结构预测任务上能很好地泛化。
Nat Commun. 2025 Jul 1;16(1):5671. doi: 10.1038/s41467-025-60872-5.
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Comprehensive benchmarking of large language models for RNA secondary structure prediction.用于RNA二级结构预测的大语言模型的全面基准测试。
Brief Bioinform. 2025 Mar 4;26(2). doi: 10.1093/bib/bbaf137.
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IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling.IPANEMAP套件：一种用于探测信息RNA结构建模的流程。
NAR Genom Bioinform. 2025 Mar 25;7(1):lqaf028. doi: 10.1093/nargab/lqaf028. eCollection 2025 Mar.
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Analyzing aptamer structure and interactions: in silico modelling and instrumental methods.分析适配体结构与相互作用：计算机模拟建模及仪器方法
Biophys Rev. 2024 Nov 20;16(6):685-700. doi: 10.1007/s12551-024-01252-z. eCollection 2024 Dec.
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Robust RNA secondary structure prediction with a mixture of deep learning and physics-based experts.结合深度学习和基于物理的专家方法进行稳健的RNA二级结构预测。
Biol Methods Protoc. 2025 Jan 6;10(1):bpae097. doi: 10.1093/biomethods/bpae097. eCollection 2025.
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DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences.诱饵序列查找器：同源RNA序列集中污染物的鉴定
bioRxiv. 2024 Oct 15:2024.10.12.618037. doi: 10.1101/2024.10.12.618037.
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Intronic RNA secondary structural information captured for the human pre-mRNA.为人类前体信使核糖核酸捕获的内含子RNA二级结构信息。
NAR Genom Bioinform. 2024 Oct 24;6(4):lqae143. doi: 10.1093/nargab/lqae143. eCollection 2024 Sep.
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Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA.利用SEARCH-MaP和SEISMIC-RNA发现并定量冠状病毒基因组中的长程RNA碱基对
Res Sq. 2024 Aug 7:rs.3.rs-4814547. doi: 10.21203/rs.3.rs-4814547/v1.
本文引用的文献
1
Kinetics coming into focus: single-molecule microscopy of riboswitch dynamics.动力学成为焦点：核酶动力学的单分子荧光显微镜研究。
RNA Biol. 2019 Sep;16(9):1077-1085. doi: 10.1080/15476286.2018.1536594. Epub 2018 Oct 29.
2
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.RFAM 13.0：转向以基因组为中心的非编码 RNA 家族资源
Nucleic Acids Res. 2018 Jan 4;46(D1):D335-D342. doi: 10.1093/nar/gkx1038.
3
Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs.碱基对概率估计提高了RNA非规范碱基对的预测准确性。
PLoS Comput Biol. 2017 Nov 6;13(11):e1005827. doi: 10.1371/journal.pcbi.1005827. eCollection 2017 Nov.
4
TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.TurboFold II：基于多个同源物的RNA结构比对与二级结构预测
Nucleic Acids Res. 2017 Nov 16;45(20):11570-11581. doi: 10.1093/nar/gkx815.
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Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data.利用序列比较和实验图谱数据构建RNA二级结构模型。
Biophys J. 2017 Jul 25;113(2):330-338. doi: 10.1016/j.bpj.2017.06.039. Epub 2017 Jul 20.
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Ensemble cryo-EM elucidates the mechanism of translation fidelity.冷冻电镜技术揭示翻译保真机制。
Nature. 2017 Jun 1;546(7656):113-117. doi: 10.1038/nature22397. Epub 2017 May 24.
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The ribosome's energy landscape: Recent insights from computation.核糖体的能量景观：计算领域的最新见解
Biophys Rev. 2015 Sep;7(3):301-310. doi: 10.1007/s12551-014-0155-1. Epub 2015 Jan 18.
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A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction.RNA折叠最近邻参数的敏感性分析确定了对RNA二级结构预测影响最大的自由能参数子集。
Nucleic Acids Res. 2017 Jun 2;45(10):6168-6176. doi: 10.1093/nar/gkx170.
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Recurring RNA structural motifs underlie the mechanics of L1 stalk movement.重复的 RNA 结构基元是 L1 茎部运动的力学基础。
Nat Commun. 2017 Feb 8;8:14285. doi: 10.1038/ncomms14285.
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Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures.环状结构形成概率的精确计算可识别RNA二级结构中的折叠基序。
RNA. 2016 Dec;22(12):1808-1818. doi: 10.1261/rna.053694.115. Epub 2016 Oct 19.
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