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For: Andronescu M, Condon A, Turner DH, Mathews DH. The determination of RNA folding nearest neighbor parameters. Methods Mol Biol 2014;1097:45-70. [PMID: 24639154 DOI: 10.1007/978-1-62703-709-9_3] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Number Cited by Other Article(s)
1
Qiu X. Robust RNA secondary structure prediction with a mixture of deep learning and physics-based experts. Biol Methods Protoc 2025;10:bpae097. [PMID: 39811444 PMCID: PMC11729747 DOI: 10.1093/biomethods/bpae097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 12/01/2024] [Accepted: 12/25/2024] [Indexed: 01/16/2025]  Open
2
Zhu M, Zuber J, Tan Z, Sharma G, Mathews DH. DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.12.618037. [PMID: 39464058 PMCID: PMC11507696 DOI: 10.1101/2024.10.12.618037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
3
von Löhneysen S, Mörl M, Stadler PF. Limits of experimental evidence in RNA secondary structure prediction. FRONTIERS IN BIOINFORMATICS 2024;4:1346779. [PMID: 38456157 PMCID: PMC10918467 DOI: 10.3389/fbinf.2024.1346779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/09/2024] [Indexed: 03/09/2024]  Open
4
Zuber J, Mathews DH. Estimating RNA Secondary Structure Folding Free Energy Changes with efn2. Methods Mol Biol 2024;2726:1-13. [PMID: 38780725 DOI: 10.1007/978-1-0716-3519-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
5
Metkar M, Pepin CS, Moore MJ. Tailor made: the art of therapeutic mRNA design. Nat Rev Drug Discov 2024;23:67-83. [PMID: 38030688 DOI: 10.1038/s41573-023-00827-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2023] [Indexed: 12/01/2023]
6
Pham TM, Miffin T, Sun H, Sharp KK, Wang X, Zhu M, Hoshika S, Peterson RJ, Benner SA, Kahn JD, Mathews DH. DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters. ACS Synth Biol 2023;12:2750-2763. [PMID: 37671922 PMCID: PMC10510751 DOI: 10.1021/acssynbio.3c00358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Indexed: 09/07/2023]
7
Pham TM, Miffin T, Sun H, Sharp KK, Wang X, Zhu M, Hoshika S, Peterson RJ, Benner SA, Kahn JD, Mathews DH. DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543917. [PMID: 37333404 PMCID: PMC10274641 DOI: 10.1101/2023.06.06.543917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
8
Poppleton E, Urbanek N, Chakraborty T, Griffo A, Monari L, Göpfrich K. RNA origami: design, simulation and application. RNA Biol 2023;20:510-524. [PMID: 37498217 PMCID: PMC10376919 DOI: 10.1080/15476286.2023.2237719] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023]  Open
9
Rolband L, Beasock D, Wang Y, Shu YG, Dinman JD, Schlick T, Zhou Y, Kieft JS, Chen SJ, Bussi G, Oukhaled A, Gao X, Šulc P, Binzel D, Bhullar AS, Liang C, Guo P, Afonin KA. Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions. Comput Struct Biotechnol J 2022;20:6120-6137. [PMID: 36420155 PMCID: PMC9672130 DOI: 10.1016/j.csbj.2022.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022]  Open
10
Szabat M, Prochota M, Kierzek R, Kierzek E, Mathews DH. A Test and Refinement of Folding Free Energy Nearest Neighbor Parameters for RNA Including N6-Methyladenosine. J Mol Biol 2022;434:167632. [PMID: 35588868 PMCID: PMC11235186 DOI: 10.1016/j.jmb.2022.167632] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/29/2022] [Accepted: 05/07/2022] [Indexed: 12/26/2022]
11
Zuber J, Schroeder SJ, Sun H, Turner DH, Mathews DH. Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects. Nucleic Acids Res 2022;50:5251-5262. [PMID: 35524574 PMCID: PMC9122537 DOI: 10.1093/nar/gkac261] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/29/2022] [Accepted: 04/08/2022] [Indexed: 12/26/2022]  Open
12
Cheng Y, Zhang S, Xu X, Chen SJ. Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding. J Phys Chem B 2021;125:10108-10118. [PMID: 34473508 DOI: 10.1021/acs.jpcb.1c04731] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
13
Zhao Q, Zhao Z, Fan X, Yuan Z, Mao Q, Yao Y. Review of machine learning methods for RNA secondary structure prediction. PLoS Comput Biol 2021;17:e1009291. [PMID: 34437528 PMCID: PMC8389396 DOI: 10.1371/journal.pcbi.1009291] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]  Open
14
Sugimoto N, Endoh T, Takahashi S, Tateishi-Karimata H. Chemical Biology of Double Helical and Non-Double Helical Nucleic Acids: “To B or Not To B, That Is the Question”. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210131] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
15
Inverse RNA Folding Workflow to Design and Test Ribozymes that Include Pseudoknots. Methods Mol Biol 2021;2167:113-143. [PMID: 32712918 DOI: 10.1007/978-1-0716-0716-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
16
Hurst T, Chen SJ. Deciphering nucleotide modification-induced structure and stability changes. RNA Biol 2021;18:1920-1930. [PMID: 33586616 DOI: 10.1080/15476286.2021.1882179] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
17
Ward M, Sun H, Datta A, Wise M, Mathews DH. Determining parameters for non-linear models of multi-loop free energy change. Bioinformatics 2020;35:4298-4306. [PMID: 30923811 DOI: 10.1093/bioinformatics/btz222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 02/10/2019] [Accepted: 03/27/2019] [Indexed: 12/12/2022]  Open
18
Liu Z, Li G, Liu JS. New Algorithms in RNA Structure Prediction Based on BHG. INT J PATTERN RECOGN 2020. [DOI: 10.1142/s0218001420500317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
19
Takahashi S, Sugimoto N. Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells. Chem Soc Rev 2020;49:8439-8468. [DOI: 10.1039/d0cs00594k] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
20
Nishida S, Sakuraba S, Asai K, Hamada M. Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2019;16:1645-1655. [PMID: 29994069 DOI: 10.1109/tcbb.2018.2813388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
21
Spasic A, Berger KD, Chen JL, Seetin MG, Turner DH, Mathews DH. Improving RNA nearest neighbor parameters for helices by going beyond the two-state model. Nucleic Acids Res 2019;46:4883-4892. [PMID: 29718397 PMCID: PMC6007268 DOI: 10.1093/nar/gky270] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/22/2018] [Indexed: 12/31/2022]  Open
22
Spasic A, Assmann SM, Bevilacqua PC, Mathews DH. Modeling RNA secondary structure folding ensembles using SHAPE mapping data. Nucleic Acids Res 2019;46:314-323. [PMID: 29177466 PMCID: PMC5758915 DOI: 10.1093/nar/gkx1057] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 10/30/2017] [Indexed: 12/22/2022]  Open
23
Steger G, Riesner D. Viroid research and its significance for RNA technology and basic biochemistry. Nucleic Acids Res 2019;46:10563-10576. [PMID: 30304486 PMCID: PMC6237808 DOI: 10.1093/nar/gky903] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/24/2018] [Indexed: 12/27/2022]  Open
24
Zuber J, Mathews DH. Estimating uncertainty in predicted folding free energy changes of RNA secondary structures. RNA (NEW YORK, N.Y.) 2019;25:747-754. [PMID: 30952689 PMCID: PMC6521603 DOI: 10.1261/rna.069203.118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
25
Ponce-Salvatierra A, Astha, Merdas K, Nithin C, Ghosh P, Mukherjee S, Bujnicki JM. Computational modeling of RNA 3D structure based on experimental data. Biosci Rep 2019;39:BSR20180430. [PMID: 30670629 PMCID: PMC6367127 DOI: 10.1042/bsr20180430] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 01/02/2023]  Open
26
Smith LG, Tan Z, Spasic A, Dutta D, Salas-Estrada LA, Grossfield A, Mathews DH. Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations. J Chem Theory Comput 2018;14:6598-6612. [PMID: 30375860 DOI: 10.1021/acs.jctc.8b00633] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
27
Zuber J, Cabral BJ, McFadyen I, Mauger DM, Mathews DH. Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction. RNA (NEW YORK, N.Y.) 2018;24:1568-1582. [PMID: 30104207 PMCID: PMC6191722 DOI: 10.1261/rna.065102.117] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 08/07/2018] [Indexed: 05/08/2023]
28
Liu Z, Zhu D, Dai Q. Predicting Model and Algorithm in RNA Folding Structure Including Pseudoknots. INT J PATTERN RECOGN 2018. [DOI: 10.1142/s0218001418510059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
29
Ward M, Datta A, Wise M, Mathews DH. Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best. Nucleic Acids Res 2017;45:8541-8550. [PMID: 28586479 PMCID: PMC5737859 DOI: 10.1093/nar/gkx512] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/31/2017] [Indexed: 01/08/2023]  Open
30
Zuber J, Sun H, Zhang X, McFadyen I, Mathews DH. 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. Nucleic Acids Res 2017;45:6168-6176. [PMID: 28334976 PMCID: PMC5449625 DOI: 10.1093/nar/gkx170] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 03/10/2017] [Indexed: 01/02/2023]  Open
31
Findeiß S, Etzel M, Will S, Mörl M, Stadler PF. Design of Artificial Riboswitches as Biosensors. SENSORS 2017;17:s17091990. [PMID: 28867802 PMCID: PMC5621056 DOI: 10.3390/s17091990] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 08/23/2017] [Accepted: 08/25/2017] [Indexed: 12/11/2022]
32
Choudhary K, Deng F, Aviran S. Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions. QUANTITATIVE BIOLOGY 2017;5:3-24. [PMID: 28717530 PMCID: PMC5510538 DOI: 10.1007/s40484-017-0093-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/08/2016] [Accepted: 12/15/2016] [Indexed: 12/30/2022]
33
Raposo AN, Gomes AJP. Computational 3D Assembling Methods for DNA: A Survey. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016;13:1068-1085. [PMID: 26701896 DOI: 10.1109/tcbb.2015.2510008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
34
Nainar S, Feng C, Spitale RC. Chemical Tools for Dissecting the Role of lncRNAs in Epigenetic Regulation. ACS Chem Biol 2016;11:2091-100. [PMID: 27267401 PMCID: PMC5068361 DOI: 10.1021/acschembio.6b00366] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
35
Bridging the gap between in vitro and in vivo RNA folding. Q Rev Biophys 2016;49:e10. [PMID: 27658939 DOI: 10.1017/s003358351600007x] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
36
Fang R, Moss WN, Rutenberg-Schoenberg M, Simon MD. Probing Xist RNA Structure in Cells Using Targeted Structure-Seq. PLoS Genet 2015;11:e1005668. [PMID: 26646615 PMCID: PMC4672913 DOI: 10.1371/journal.pgen.1005668] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/24/2015] [Indexed: 11/19/2022]  Open
37
Wagner D, Rinnenthal J, Narberhaus F, Schwalbe H. Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution. Nucleic Acids Res 2015;43:5572-85. [PMID: 25940621 PMCID: PMC4477652 DOI: 10.1093/nar/gkv414] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/08/2015] [Indexed: 12/16/2022]  Open
38
Sloma MF, Mathews DH. Improving RNA secondary structure prediction with structure mapping data. Methods Enzymol 2015;553:91-114. [PMID: 25726462 DOI: 10.1016/bs.mie.2014.10.053] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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