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For: Cao S, Chen SJ. Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal. RNA 2011;17:2130-43. [PMID: 22028361 PMCID: PMC3222126 DOI: 10.1261/rna.026658.111] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 09/12/2011] [Indexed: 05/24/2023]
Number Cited by Other Article(s)
1
Wang F, Xia R, Su Y, Cai P, Xu X. Quantifying RNA structures and interactions with a unified reduced chain representation model. Int J Biol Macromol 2023;253:127181. [PMID: 37793523 DOI: 10.1016/j.ijbiomac.2023.127181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/30/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023]
2
Zhang D, Gong L, Weng J, Li Y, Wang A, Li G. RNA Folding Based on 5 Beads Model and Multiscale Simulation. Interdiscip Sci 2023:10.1007/s12539-023-00561-3. [PMID: 37115389 DOI: 10.1007/s12539-023-00561-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 04/29/2023]
3
Wang F, Li W, Li B, Xie L, Tong Y, Xu X. cRNAsp12 Web Server for the Prediction of Circular RNA Secondary Structures and Stabilities. Int J Mol Sci 2023;24:ijms24043822. [PMID: 36835231 PMCID: PMC9959564 DOI: 10.3390/ijms24043822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/29/2023] [Accepted: 02/07/2023] [Indexed: 02/17/2023]  Open
4
Kensinger AH, Makowski JA, Pellegrene KA, Imperatore JA, Cunningham CL, Frye CJ, Lackey PE, Mihailescu MR, Evanseck JD. Structural, Dynamical, and Entropic Differences between SARS-CoV and SARS-CoV-2 s2m Elements Using Molecular Dynamics Simulations. ACS PHYSICAL CHEMISTRY AU 2023;3:30-43. [PMID: 36711027 PMCID: PMC9578647 DOI: 10.1021/acsphyschemau.2c00032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/05/2022]
5
A liquid crystal world for the origins of life. Emerg Top Life Sci 2022;6:557-569. [PMID: 36373852 DOI: 10.1042/etls20220081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022]
6
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
7
Zhang D, Li Y, Zhong Q, Wang A, Weng J, Gong L, Li G. Ribonucleic Acid Folding Prediction Based on Iterative Multiscale Simulation. J Phys Chem Lett 2022;13:9957-9966. [PMID: 36260782 DOI: 10.1021/acs.jpclett.2c01342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
8
Zhang S, Cheng Y, Guo P, Chen SJ. VfoldMCPX: predicting multistrand RNA complexes. RNA (NEW YORK, N.Y.) 2022;28:596-608. [PMID: 35058350 PMCID: PMC8925972 DOI: 10.1261/rna.079020.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
9
Xu X, Jin L, Xie L, Chen SJ. Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding. J Chem Theory Comput 2022;18:2002-2015. [PMID: 35133833 DOI: 10.1021/acs.jctc.1c01233] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
10
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]
11
Song Z, Gremminger T, Singh G, Cheng Y, Li J, Qiu L, Ji J, Lange MJ, Zuo X, Chen SJ, Zou X, Boris-Lawrie K, Heng X. The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity. Nucleic Acids Res 2021;49:5925-5942. [PMID: 33978756 PMCID: PMC8191761 DOI: 10.1093/nar/gkab342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/24/2022]  Open
12
A malachite green light-up aptasensor for the detection of theophylline. Talanta 2021;232:122417. [PMID: 34074405 DOI: 10.1016/j.talanta.2021.122417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/01/2021] [Accepted: 04/08/2021] [Indexed: 11/24/2022]
13
Ju C, Wang M, Tak E, Kim B, Emontzpohl C, Yang Y, Yuan X, Kutay H, Liang Y, Hall DR, Dar WA, Bynon JS, Carmeliet P, Ghoshal K, Eltzschig HK. Hypoxia-inducible factor-1α-dependent induction of miR122 enhances hepatic ischemia tolerance. J Clin Invest 2021;131:140300. [PMID: 33792566 PMCID: PMC8011886 DOI: 10.1172/jci140300] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 02/10/2021] [Indexed: 12/29/2022]  Open
14
Zhang D, Li J, Chen SJ. IsRNA1: De Novo Prediction and Blind Screening of RNA 3D Structures. J Chem Theory Comput 2021;17:1842-1857. [PMID: 33560836 DOI: 10.1021/acs.jctc.0c01148] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
15
Zhao C, Zhang D, Jiang Y, Chen SJ. Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability. Biophys J 2020;119:1439-1455. [PMID: 32949490 PMCID: PMC7568001 DOI: 10.1016/j.bpj.2020.07.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/12/2020] [Accepted: 07/08/2020] [Indexed: 12/21/2022]  Open
16
Xu X, Chen SJ. Topological constraints of RNA pseudoknotted and loop-kissing motifs: applications to three-dimensional structure prediction. Nucleic Acids Res 2020;48:6503-6512. [PMID: 32491164 PMCID: PMC7337929 DOI: 10.1093/nar/gkaa463] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 05/19/2020] [Indexed: 01/23/2023]  Open
17
Jin L, Tan YL, Wu Y, Wang X, Shi YZ, Tan ZJ. Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway. RNA (NEW YORK, N.Y.) 2019;25:1532-1548. [PMID: 31391217 PMCID: PMC6795135 DOI: 10.1261/rna.071662.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/02/2019] [Indexed: 05/08/2023]
18
Murata A, Nakamori M, Nakatani K. Modulating RNA secondary and tertiary structures by mismatch binding ligands. Methods 2019;167:78-91. [DOI: 10.1016/j.ymeth.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 12/21/2022]  Open
19
Kimchi O, Cragnolini T, Brenner MP, Colwell LJ. A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots. Biophys J 2019;117:520-532. [PMID: 31353036 PMCID: PMC6697467 DOI: 10.1016/j.bpj.2019.06.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 06/21/2019] [Accepted: 06/27/2019] [Indexed: 11/18/2022]  Open
20
Hamachi K, Mutsuro-Aoki H, Tanizawa K, Hirasawa I, Umehara T, Tamura K. Effects of complementary loop composition in truncated R3C ligase ribozymes on kiss switch activation. Biosystems 2019;177:9-15. [PMID: 30639771 DOI: 10.1016/j.biosystems.2019.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/04/2019] [Accepted: 01/07/2019] [Indexed: 12/24/2022]
21
Thermodynamic investigation of kissing-loop interactions. Biochimie 2018;157:177-183. [PMID: 30502370 DOI: 10.1016/j.biochi.2018.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/20/2018] [Indexed: 01/01/2023]
22
Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018;118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 386] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
23
Zhao C, Xu X, Chen SJ. Predicting RNA Structure with Vfold. Methods Mol Biol 2017;1654:3-15. [PMID: 28986779 PMCID: PMC5762135 DOI: 10.1007/978-1-4939-7231-9_1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
24
Xu X, Chen SJ. VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability. PLoS One 2016;11:e0163454. [PMID: 27657918 PMCID: PMC5033388 DOI: 10.1371/journal.pone.0163454] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/08/2016] [Indexed: 12/25/2022]  Open
25
Structural computational modeling of RNA aptamers. Methods 2016;103:175-9. [PMID: 26972787 DOI: 10.1016/j.ymeth.2016.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 01/10/2023]  Open
26
Crucial steps to life: From chemical reactions to code using agents. Biosystems 2016;140:49-57. [DOI: 10.1016/j.biosystems.2015.12.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/05/2015] [Accepted: 12/07/2015] [Indexed: 01/21/2023]
27
Barth A, Kobbe D, Focke M. DNA-DNA kissing complexes as a new tool for the assembly of DNA nanostructures. Nucleic Acids Res 2016;44:1502-13. [PMID: 26773051 PMCID: PMC4770242 DOI: 10.1093/nar/gkw014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 01/06/2016] [Indexed: 12/14/2022]  Open
28
Xu X, Chen SJ. A Method to Predict the Structure and Stability of RNA/RNA Complexes. Methods Mol Biol 2016;1490:63-72. [PMID: 27665593 DOI: 10.1007/978-1-4939-6433-8_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
29
Xu X, Chen SJ. Physics-based RNA structure prediction. BIOPHYSICS REPORTS 2015;1:2-13. [PMID: 26942214 PMCID: PMC4762127 DOI: 10.1007/s41048-015-0001-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 02/16/2015] [Indexed: 12/15/2022]  Open
30
Xu X, Chen SJ. A Method to Predict the 3D Structure of an RNA Scaffold. Methods Mol Biol 2015;1316:1-11. [PMID: 25967048 PMCID: PMC5512611 DOI: 10.1007/978-1-4939-2730-2_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
31
Xu X, Zhao P, Chen SJ. Vfold: a web server for RNA structure and folding thermodynamics prediction. PLoS One 2014;9:e107504. [PMID: 25215508 PMCID: PMC4162592 DOI: 10.1371/journal.pone.0107504] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/11/2014] [Indexed: 11/19/2022]  Open
32
Zhu Y, Chen SJ. Many-body effect in ion binding to RNA. J Chem Phys 2014;141:055101. [PMID: 25106614 PMCID: PMC4119196 DOI: 10.1063/1.4890656] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/30/2014] [Indexed: 01/07/2023]  Open
33
Cao S, Xu X, Chen SJ. Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing. RNA (NEW YORK, N.Y.) 2014;20:835-45. [PMID: 24751648 PMCID: PMC4024638 DOI: 10.1261/rna.043976.113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 02/23/2014] [Indexed: 05/24/2023]
34
Hong C, Otabe T, Matsumoto S, Dohno C, Murata A, Hagihara M, Nakatani K. Formation of a Ligand-Assisted Complex of Two RNA Hairpin Loops. Chemistry 2014;20:5282-7. [DOI: 10.1002/chem.201304683] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Indexed: 01/16/2023]
35
He Z, Zhu Y, Chen SJ. Exploring the electrostatic energy landscape for tetraloop-receptor docking. Phys Chem Chem Phys 2013;16:6367-75. [PMID: 24322001 DOI: 10.1039/c3cp53655f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
36
Stephenson JD, Li H, Kenyon JC, Symmons M, Klenerman D, Lever AML. Three-dimensional RNA structure of the major HIV-1 packaging signal region. Structure 2013;21:951-62. [PMID: 23685210 PMCID: PMC3690526 DOI: 10.1016/j.str.2013.04.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 03/23/2013] [Accepted: 04/03/2013] [Indexed: 12/04/2022]
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