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10.1093/nar/gkab119 http://scihub22266oqcxt.onion/10.1093/nar/gkab119 33693814!8034642!33693814     free     free     free Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 233.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       Nucleic+Acids+Res 2021 ; 49 (6): 3092-3108 Nephropedia Template TP {{tp|p=33693814|t=2021. De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures |pdf=|usr=}}{{33693814}} gab.com Text De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures JO: Nucleic Acids Res http://www.kidney.de/pget.php?&tw=1&pmid=33693814 #FOAvip The rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA elements that offer potential small-molecule drug targets, but most of their 3D structures have not been experimentally characterized. Here, we provide a compilation of chemical mapping data from our and other labs, secondary structure models, and 3D model ensembles based on Rosetta's FARFAR2 algorithm for SARS-CoV-2 RNA regions including the individual stems SL1-8 in the extended 5' UTR; the reverse complement of the 5' UTR SL1-4; the frameshift stimulating element (FSE); and the extended pseudoknot, hypervariable region, and s2m of the 3' UTR. For eleven of these elements (the stems in SL1-8, reverse complement of SL1-4, FSE, s2m and 3' UTR pseudoknot), modeling convergence supports the accuracy of predicted low energy states; subsequent cryo-EM characterization of the FSE confirms modeling accuracy. To aid efforts to discover small molecule RNA binders guided by computational models, we provide a second set of similarly prepared models for RNA riboswitches that bind small molecules. Both datasets ('FARFAR2-SARS-CoV-2', https://github.com/DasLab/FARFAR2-SARS-CoV-2; and 'FARFAR2-Apo-Riboswitch', at https://github.com/DasLab/FARFAR2-Apo-Riboswitch') include up to 400 models for each RNA element, which may facilitate drug discovery approaches targeting dynamic ensembles of RNA molecules. Twit Text FOAVip De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures ????Nucleic Acids Res http://www.kidney.de/pget.php?&tw=1&pmid=33693814 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=33693814 #FOAvip English Wikipedia <ref>{{Cite pmid|33693814}}</ref> De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures #MMPMID33693814 Rangan R; Watkins AM; Chacon J; Kretsch R; Kladwang W; Zheludev IN; Townley J; Rynge M; Thain G; Das R Nucleic Acids Res 2021[Apr]; 49 (6): 3092-3108 PMID33693814show ga The rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA elements that offer potential small-molecule drug targets, but most of their 3D structures have not been experimentally characterized. Here, we provide a compilation of chemical mapping data from our and other labs, secondary structure models, and 3D model ensembles based on Rosetta's FARFAR2 algorithm for SARS-CoV-2 RNA regions including the individual stems SL1-8 in the extended 5' UTR; the reverse complement of the 5' UTR SL1-4; the frameshift stimulating element (FSE); and the extended pseudoknot, hypervariable region, and s2m of the 3' UTR. For eleven of these elements (the stems in SL1-8, reverse complement of SL1-4, FSE, s2m and 3' UTR pseudoknot), modeling convergence supports the accuracy of predicted low energy states; subsequent cryo-EM characterization of the FSE confirms modeling accuracy. To aid efforts to discover small molecule RNA binders guided by computational models, we provide a second set of similarly prepared models for RNA riboswitches that bind small molecules. Both datasets ('FARFAR2-SARS-CoV-2', https://github.com/DasLab/FARFAR2-SARS-CoV-2; and 'FARFAR2-Apo-Riboswitch', at https://github.com/DasLab/FARFAR2-Apo-Riboswitch') include up to 400 models for each RNA element, which may facilitate drug discovery approaches targeting dynamic ensembles of RNA molecules. |*Consensus[MESH] |*Models, Molecular[MESH] |*Nucleic Acid Conformation[MESH] |3' Untranslated Regions/genetics[MESH] |5' Untranslated Regions/genetics[MESH] |Algorithms[MESH] |Aptamers, Nucleotide/genetics[MESH] |Base Sequence[MESH] |Binding Sites[MESH] |Cryoelectron Microscopy[MESH] |Datasets as Topic[MESH] |Drug Evaluation, Preclinical/methods[MESH] |Frameshifting, Ribosomal/genetics[MESH] |Genome, Viral/genetics[MESH] |RNA Stability[MESH] |RNA, Viral/*chemistry/genetics[MESH] |Reproducibility of Results[MESH] |Riboswitch/genetics[MESH] |SARS-CoV-2/*genetics[MESH]De novo 3D models of SARS-CoV-2 RNA elements from consensus experiment(epmc).pdf DeepDyve Pubget Overpricing