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For: Li B, Cao Y, Westhof E, Miao Z. Advances in RNA 3D Structure Modeling Using Experimental Data. Front Genet 2020;11:574485. [PMID: 33193680 PMCID: PMC7649352 DOI: 10.3389/fgene.2020.574485] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/02/2020] [Indexed: 12/26/2022]  Open
Number Cited by Other Article(s)
1
Moafinejad SN, de Aquino BRH, Boniecki M, Pandaranadar Jeyeram IN, Nikolaev G, Magnus M, Farsani M, Badepally N, Wirecki T, Stefaniak F, Bujnicki J. SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories. Nucleic Acids Res 2024;52:W368-W373. [PMID: 38738621 PMCID: PMC11223799 DOI: 10.1093/nar/gkae356] [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: 02/28/2024] [Revised: 04/07/2024] [Accepted: 04/29/2024] [Indexed: 05/14/2024]  Open
2
Bernard C, Postic G, Ghannay S, Tahi F. State-of-the-RNArt: benchmarking current methods for RNA 3D structure prediction. NAR Genom Bioinform 2024;6:lqae048. [PMID: 38745991 PMCID: PMC11091930 DOI: 10.1093/nargab/lqae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/05/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]  Open
3
Trinity L, Stege U, Jabbari H. Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot. PLoS Comput Biol 2024;20:e1011787. [PMID: 38713726 PMCID: PMC11108256 DOI: 10.1371/journal.pcbi.1011787] [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: 12/27/2023] [Revised: 05/21/2024] [Accepted: 04/27/2024] [Indexed: 05/09/2024]  Open
4
Irving PS, Weeks KM. RNAvigate: efficient exploration of RNA chemical probing datasets. Nucleic Acids Res 2024;52:2231-2241. [PMID: 38348910 PMCID: PMC10954457 DOI: 10.1093/nar/gkae089] [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: 04/30/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024]  Open
5
Thiel BC, Poblete S, Hofacker IL. The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline. Methods Mol Biol 2024;2726:377-399. [PMID: 38780739 DOI: 10.1007/978-1-0716-3519-3_15] [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] [Indexed: 05/25/2024]
6
Wu P, Yang L. sRNA Structural Modeling Based on NMR Data. Methods Mol Biol 2024;2741:383-397. [PMID: 38217664 DOI: 10.1007/978-1-0716-3565-0_20] [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] [Indexed: 01/15/2024]
7
Levintov L, Vashisth H. Structural and computational studies of HIV-1 RNA. RNA Biol 2024;21:1-32. [PMID: 38100535 PMCID: PMC10730233 DOI: 10.1080/15476286.2023.2289709] [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] [Accepted: 11/21/2023] [Indexed: 12/17/2023]  Open
8
Irving PS, Weeks KM. RNAvigate: Efficient exploration of RNA chemical probing datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538311. [PMID: 37162917 PMCID: PMC10168276 DOI: 10.1101/2023.04.25.538311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
9
Tieng FYF, Abdullah-Zawawi MR, Md Shahri NAA, Mohamed-Hussein ZA, Lee LH, Mutalib NSA. A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools. Brief Bioinform 2023;25:bbad421. [PMID: 38040490 PMCID: PMC10753535 DOI: 10.1093/bib/bbad421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 12/03/2023]  Open
10
Kuhle B, Chen Q, Schimmel P. tRNA renovatio: Rebirth through fragmentation. Mol Cell 2023;83:3953-3971. [PMID: 37802077 PMCID: PMC10841463 DOI: 10.1016/j.molcel.2023.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023]
11
Rahaman MM, Khan NS, Zhang S. RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families. Bioinformatics 2023;39:i337-i346. [PMID: 37387191 DOI: 10.1093/bioinformatics/btad223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]  Open
12
Quadrini M, Tesei L, Merelli E. Automatic generation of pseudoknotted RNAs taxonomy. BMC Bioinformatics 2023;23:575. [PMID: 37322429 DOI: 10.1186/s12859-023-05362-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/25/2023] [Indexed: 06/17/2023]  Open
13
Kamga Youmbi FI, Kengne Tchendji V, Tayou Djamegni C. P-FARFAR2: A multithreaded greedy approach to sampling low-energy RNA structures in Rosetta FARFAR2. Comput Biol Chem 2023;104:107878. [PMID: 37167861 DOI: 10.1016/j.compbiolchem.2023.107878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/23/2023] [Accepted: 05/01/2023] [Indexed: 05/13/2023]
14
How does precursor RNA structure influence RNA processing and gene expression? Biosci Rep 2023;43:232489. [PMID: 36689327 PMCID: PMC9977717 DOI: 10.1042/bsr20220149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 01/24/2023]  Open
15
Sabei A, Caldas Baia TG, Saffar R, Martin J, Frezza E. Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes. J Chem Inf Model 2023;63:2554-2572. [PMID: 36972178 DOI: 10.1021/acs.jcim.2c01509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
16
Trinity L, Wark I, Lansing L, Jabbari H, Stege U. Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot. PLoS Comput Biol 2023;19:e1010922. [PMID: 36854032 PMCID: PMC10004594 DOI: 10.1371/journal.pcbi.1010922] [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: 10/04/2022] [Revised: 03/10/2023] [Accepted: 02/05/2023] [Indexed: 03/02/2023]  Open
17
Ma H, Pham P, Luo B, Rangan R, Kappel K, Su Z, Das R. Auto-DRRAFTER: Automated RNA Modeling Based on Cryo-EM Density. Methods Mol Biol 2023;2568:193-211. [PMID: 36227570 DOI: 10.1007/978-1-0716-2687-0_13] [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: 05/14/2023]
18
Schuster P, Stadler PF. Virus Evolution on Fitness Landscapes. Curr Top Microbiol Immunol 2023;439:1-94. [PMID: 36592242 DOI: 10.1007/978-3-031-15640-3_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
19
Myatt DP, Wharram L, Graham C, Liddell J, Branton H, Pizzey C, Cowieson N, Rambo R, Shattock RJ. Biophysical characterization of the structure of a SARS-CoV-2 self-amplifying RNA (saRNA) vaccine. Biol Methods Protoc 2023;8:bpad001. [PMID: 36915370 PMCID: PMC10008065 DOI: 10.1093/biomethods/bpad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/13/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023]  Open
20
Catacalos C, Krohannon A, Somalraju S, Meyer KD, Janga SC, Chakrabarti K. Epitranscriptomics in parasitic protists: Role of RNA chemical modifications in posttranscriptional gene regulation. PLoS Pathog 2022;18:e1010972. [PMID: 36548245 PMCID: PMC9778586 DOI: 10.1371/journal.ppat.1010972] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
21
Liang W, Wang S, Wang H, Li X, Meng Q, Zhao Y, Zheng C. When 3D genome technology meets viral infection, including SARS-CoV-2. J Med Virol 2022;94:5627-5639. [PMID: 35916043 PMCID: PMC9538846 DOI: 10.1002/jmv.28040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/09/2022] [Accepted: 07/30/2022] [Indexed: 01/06/2023]
22
Huang Y, Luo J, Jing R, Li M. Multi-model predictive analysis of RNA solvent accessibility based on modified residual attention mechanism. Brief Bioinform 2022;23:6775603. [PMID: 36305428 DOI: 10.1093/bib/bbac470] [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: 06/30/2022] [Revised: 09/09/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022]  Open
23
Sharma P, Mondal K, Kumar S, Tamang S, Najar IN, Das S, Thakur N. RNA thermometers in bacteria: Role in thermoregulation. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - GENE REGULATORY MECHANISMS 2022;1865:194871. [DOI: 10.1016/j.bbagrm.2022.194871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/09/2022] [Accepted: 08/21/2022] [Indexed: 04/09/2023]
24
Matarrese MAG, Loppini A, Nicoletti M, Filippi S, Chiodo L. Assessment of tools for RNA secondary structure prediction and extraction: a final-user perspective. J Biomol Struct Dyn 2022:1-20. [DOI: 10.1080/07391102.2022.2116110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
25
Mukherjee D, Maiti S, Gouda PK, Sharma R, Roy P, Bhattacharyya D. RNABPDB: Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction. Interdiscip Sci 2022;14:759-774. [PMID: 35705797 DOI: 10.1007/s12539-022-00528-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
26
Gumna J, Antczak M, Adamiak RW, Bujnicki JM, Chen SJ, Ding F, Ghosh P, Li J, Mukherjee S, Nithin C, Pachulska-Wieczorek K, Ponce-Salvatierra A, Popenda M, Sarzynska J, Wirecki T, Zhang D, Zhang S, Zok T, Westhof E, Miao Z, Szachniuk M, Rybarczyk A. Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models. Int J Mol Sci 2022;23:ijms23179630. [PMID: 36077037 PMCID: PMC9455975 DOI: 10.3390/ijms23179630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 01/19/2023]  Open
27
Ma H, Wen H, Xue Z, Li G, Zhang Z. RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites. PLoS Comput Biol 2022;18:e1010293. [PMID: 35819951 PMCID: PMC9275694 DOI: 10.1371/journal.pcbi.1010293] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 06/09/2022] [Indexed: 11/19/2022]  Open
28
Wiedemann J, Kaczor J, Milostan M, Zok T, Blazewicz J, Szachniuk M, Antczak M. RNAloops: a database of RNA multiloops. Bioinformatics 2022;38:4200-4205. [PMID: 35809063 PMCID: PMC9438955 DOI: 10.1093/bioinformatics/btac484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/26/2022] [Accepted: 07/06/2022] [Indexed: 12/24/2022]  Open
29
Li X, Bhullar AS, Binzel DW, Guo P. The dynamic, motile and deformative properties of RNA nanoparticles facilitate the third milestone of drug development. Adv Drug Deliv Rev 2022;186:114316. [PMID: 35526663 DOI: 10.1016/j.addr.2022.114316] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/25/2022] [Accepted: 04/29/2022] [Indexed: 12/13/2022]
30
Giarimoglou N, Kouvela A, Patsi I, Zhang J, Stamatopoulou V, Stathopoulos C. Lineage-specific insertions in T-box riboswitches modulate antibiotic binding and action. Nucleic Acids Res 2022;50:5834-5849. [PMID: 35580054 PMCID: PMC9177973 DOI: 10.1093/nar/gkac359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/21/2022] [Accepted: 05/11/2022] [Indexed: 01/27/2023]  Open
31
From single-omics to interactomics: How can ligand-induced perturbations modulate single-cell phenotypes? ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022;131:45-83. [PMID: 35871896 DOI: 10.1016/bs.apcsb.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
32
Solayman M, Litfin T, Singh J, Paliwal K, Zhou Y, Zhan J. Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives. Brief Bioinform 2022;23:6554125. [PMID: 35348613 PMCID: PMC9116373 DOI: 10.1093/bib/bbac112] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/30/2022]  Open
33
Olson SW, Turner AMW, Arney JW, Saleem I, Weidmann CA, Margolis DM, Weeks KM, Mustoe AM. Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP. Mol Cell 2022;82:1708-1723.e10. [PMID: 35320755 PMCID: PMC9081252 DOI: 10.1016/j.molcel.2022.02.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/29/2021] [Accepted: 02/02/2022] [Indexed: 12/17/2022]
34
He W, Henning-Knechtel A, Kirmizialtin S. Visualizing RNA Structures by SAXS-Driven MD Simulations. FRONTIERS IN BIOINFORMATICS 2022;2:781949. [PMID: 36304317 PMCID: PMC9580860 DOI: 10.3389/fbinf.2022.781949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/04/2022] [Indexed: 12/26/2022]  Open
35
Przanowska RK, Weidmann CA, Saha S, Cichewicz MA, Jensen KN, Przanowski P, Irving PS, Janes KA, Guertin MJ, Weeks KM, Dutta A. Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors. Cell Rep 2022;38:110361. [PMID: 35172143 PMCID: PMC8937029 DOI: 10.1016/j.celrep.2022.110361] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/03/2021] [Accepted: 01/19/2022] [Indexed: 12/27/2022]  Open
36
Carrascoza F, Antczak M, Miao Z, Westhof E, Szachniuk M. Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions. RNA (NEW YORK, N.Y.) 2022;28:250-262. [PMID: 34819324 PMCID: PMC8906551 DOI: 10.1261/rna.078685.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
37
Zeke A, Schád É, Horváth T, Abukhairan R, Szabó B, Tantos A. Deep structural insights into RNA-binding disordered protein regions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022;13:e1714. [PMID: 35098694 PMCID: PMC9539567 DOI: 10.1002/wrna.1714] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/22/2021] [Accepted: 01/07/2022] [Indexed: 12/11/2022]
38
Poblete S, Božič A, Kanduč M, Podgornik R, Guzman HV. RNA Secondary Structures Regulate Adsorption of Fragments onto Flat Substrates. ACS OMEGA 2021;6:32823-32831. [PMID: 34901632 PMCID: PMC8655909 DOI: 10.1021/acsomega.1c04774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
39
Poblete S, Guzman HV. Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models. Viruses 2021;13:1555. [PMID: 34452420 PMCID: PMC8402887 DOI: 10.3390/v13081555] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023]  Open
40
Li J, Chen SJ. RNA 3D Structure Prediction Using Coarse-Grained Models. Front Mol Biosci 2021;8:720937. [PMID: 34277713 PMCID: PMC8283274 DOI: 10.3389/fmolb.2021.720937] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022]  Open
41
Christy TW, Giannetti CA, Houlihan G, Smola MJ, Rice GM, Wang J, Dokholyan NV, Laederach A, Holliger P, Weeks KM. Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP. Biochemistry 2021;60:1971-1982. [PMID: 34121404 PMCID: PMC8256721 DOI: 10.1021/acs.biochem.1c00270] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Weeks KM. SHAPE Directed Discovery of New Functions in Large RNAs. Acc Chem Res 2021;54:2502-2517. [PMID: 33960770 DOI: 10.1021/acs.accounts.1c00118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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An RNA-centric historical narrative around the Protein Data Bank. J Biol Chem 2021;296:100555. [PMID: 33744291 PMCID: PMC8080527 DOI: 10.1016/j.jbc.2021.100555] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/17/2021] [Accepted: 03/16/2021] [Indexed: 01/06/2023]  Open
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