Topic 05 -- Abstracts with Biological Entities (English) - 75 Topics / Sub-Topic Model 19 - 15 Topics

cite ad title authors publish year publish time dataset abstract mentions covid pmcid pubmed id doi cord uid topic weight Similarity scispacy Similarity specter
1 Kierzek_2006 Nearest neighbor parameters for Watson–Crick complementary heteroduplexes formed between 2′-O-methyl RNA and RNA oligonucleotides Kierzek, Elzbieta; Mathews, David H.; Ciesielska, Anna; Turner, Douglas H.; Kierzek, Ryszard 2006 2006-07-26 PMC N PMC1540717 16870722.0 10.1093/nar/gkl232 sztzrx1l 0.963082 Guo_Y_2013, Staple_2005, Krause_1987 Cornish_2006, Vasquez-Del_Carpio_2006, Su_L_1999
2 Hori_2016 Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension Naoto Hori; Natalia A. Denesyuk; D. Thirumalai 2016 2016-04-15 BioRxiv N 10.1101/048801 08mep8hm 0.940947 Guo_Y_2013, Morikawa_1992, Hatfield_1990 Hori_2016, Cornish_2006
3 Theimer_1999 Equilibrium unfolding pathway of an H-type RNA pseudoknot which promotes programmed −1 ribosomal frameshifting 1 1 Edited by D. E. Draper Theimer, Carla A.; Giedroc, David P. 1999 1999-06-25 PMC N PMC7126474 10373368.0 10.1006/jmbi.1999.2850 8jzoymfy 0.900017 Morikawa_1992, Guo_Y_2013, Atkins_1999, Brierley_1991, Hatfield_1990 Marczinke_1998, Zhong_2016, Marcheschi_2007
4 Su_L_1999 Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot Su, Li; Chen, Liqing; Egli, Martin; Berger, James M.; Rich, Alexander 1999 1999-01-01 PMC N PMC7097825 10074948.0 10.1038/6722 93qae2al 0.896265 Morikawa_1992, Guo_Y_2013, Brierley_1991, Brierley_1989 Cornish_2006, Marcheschi_2007
5 Hori_2016 Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension Hori, Naoto; Denesyuk, Natalia A.; Thirumalai, D. 2016 2016-07-01 PMC N PMC5590673 27315694.0 10.1016/j.jmb.2016.06.002 x28cxlm3 0.895626 Guo_Y_2013, Morikawa_1992, Hatfield_1990 Hori_2016, Cornish_2006
6 Kierzek_2005 The influence of locked nucleic acid residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes Kierzek, Elzbieta; Ciesielska, Anna; Pasternak, Karol; Mathews, David H.; Turner, Douglas H.; Kierzek, Ryszard 2005 2005-09-09 PMC N PMC1201327 16155181.0 10.1093/nar/gki789 cl9gpt9w 0.892366 Kierzek_2006, Stork_2011, Krause_1987
7 Puglisi_1990 Conformation of an RNA pseudoknot Puglisi, Joseph D.; Wyatt, Jacqueline R.; Tinoco, Ignacio 1990 1990-07-20 PMC N 1696318.0 10.1016/0022-2836(90)90192-o ps4y6kri 0.860197 Kierzek_2006, Guo_Y_2013, Atkins_1999 Cornish_2006
8 Guo_Y_2013 Molecular dynamics simulation of RNA pseudoknot unfolding pathway Guo, Yun; Zhang, Wenbing 2013 2013-03-12 PMC N PMC7149040 10.1007/s11859-013-0905-0 2fkghukw 0.857899 Stork_2011, Pong_2011, Atkins_1999, Staple_2005 Green_2008
9 Liphardt_1999 Evidence for an RNA pseudoknot loop-helix interaction essential for efficient −1 ribosomal frameshifting 1 1 Edited by D. E. Draper Liphardt, Jan; Napthine, Sawsan; Kontos, Harry; Brierley, Ian 1999 1999-05-07 PMC N PMC7141562 10329145.0 10.1006/jmbi.1999.2689 z4mgtb6s 0.813215 Morikawa_1992, Brierley_1989, Hatfield_1990, Brierley_1991, Krause_1987 Napthine_1999, Marczinke_1998
10 Cornish_2006 Pairwise coupling analysis of helical junction hydrogen bonding interactions in luteoviral RNA pseudoknots Cornish, Peter V.; Giedroc, David P. 2006 2006-09-01 PMC N PMC2573051 16964977.0 10.1021/bi060430n n7o7x9ta 0.811094 Morikawa_1992, Stork_2011, Krause_1987, Guo_Y_2013, Pong_2011 Vasquez-Del_Carpio_2006
11 Michiels_2001 Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting 1 1 Edited by I. Tinoco Michiels, Paul J.A; Versleijen, Alexandra A.M; Verlaan, Paul W; Pleij, Cornelis W.A; Hilbers, Cornelis W; Heus, Hans A 2001 2001-07-27 PMC N 11501999.0 10.1006/jmbi.2001.4823 4g8qtlfs 0.772868 Morikawa_1992, Brierley_1989, Hatfield_1990, Brierley_1991, Atkins_1999
12 Napthine_1999 The role of RNA pseudoknot stem 1 length in the promotion of efficient −1 ribosomal frameshifting 1 1 Edited by D. E. Draper Napthine, Sawsan; Liphardt, Jan; Bloys, Alison; Routledge, Samantha; Brierley, Ian 1999 1999-05-07 PMC N PMC7126229 10329144.0 10.1006/jmbi.1999.2688 thsmrnrc 0.770519 Morikawa_1992, Hatfield_1990, Krause_1987, Brierley_1989, Firth_2009 Marczinke_1998, Liphardt_1999
13 Liu_B_2009 Fluorescence Competition Assay Measurements of Free Energy Changes for RNA Pseudoknots Liu, Biao; Shankar, Neelaabh; Turner, Douglas H. 2009 2009-11-18 None N PMC2808147 19921809.0 10.1021/bi901541j zwgnkegf 0.761028 Guo_Y_2013, Kierzek_2006, Brierley_1991 Cornish_2006, Hori_2016, Theimer_1999
14 Patil_2018 Incorporating uracil and 5-halouracils into short peptide nucleic acids for enhanced recognition of A–U pairs in dsRNAs Patil, Kiran M; Toh, Desiree-Faye Kaixin; Yuan, Zhen; Meng, Zhenyu; Shu, Zhiyu; Zhang, Haiping; Ong, Alan Ann Lerk; Krishna, Manchugondanahalli S; Lu, Lanyuan; Lu, Yunpeng; Chen, Gang 2018 2018-09-06 None N PMC6125629 30011039.0 10.1093/nar/gky631 lm7r3o3n 0.750500 Stork_2011, Kierzek_2006, Pong_2011, Guo_Y_2013
15 Olsthoorn_2010 Functional analysis of the SRV-1 RNA frameshifting pseudoknot Olsthoorn, René C. L.; Reumerman, Richard; Hilbers, Cornelis W.; Pleij, Cornelis W. A.; Heus, Hans A. 2010 2010-07-17 NONCOMM N PMC2995055 20639537.0 10.1093/nar/gkq629 8crvjzz4 0.739013 Morikawa_1992, Kang_1998, Hatfield_1990, Jacks_1988, Brierley_1989 Brierley_1991, Marczinke_1998, Li_L_2001
16 Yu_C_2011 Stem–loop structures can effectively substitute for an RNA pseudoknot in −1 ribosomal frameshifting Yu, Chien-Hung; Noteborn, Mathieu H.; Pleij, Cornelis W. A.; Olsthoorn, René C. L. 2011 2011-07-29 NONCOMM N PMC3203594 21803791.0 10.1093/nar/gkr579 wifs97yy 0.736435 Morikawa_1992, Marcheschi_2007, Stork_2011, Brierley_1991, Pong_2011 Marczinke_1998, Marcheschi_2007, Chou_2009, Cornish_2006
17 Zhong_2016 Mechanical unfolding kinetics of the SRV-1 gag-pro mRNA pseudoknot: possible implications for −1 ribosomal frameshifting stimulation Zhong, Zhensheng; Yang, Lixia; Zhang, Haiping; Shi, Jiahao; Vandana, J. Jeya; Lam, Do Thuy Uyen Ha; Olsthoorn, René C. L.; Lu, Lanyuan; Chen, Gang 2016 2016-12-21 None N PMC5175198 28000744.0 10.1038/srep39549 nr2xmcs0 0.679927 Morikawa_1992, Stork_2011, Guo_Y_2013, Brierley_1989, Pong_2011 Theimer_1999, Marczinke_1998, Marcheschi_2007, Sasvari_2011
18 Green_2008 Characterization of the Mechanical Unfolding of RNA Pseudoknots Green, Lisa; Kim, Chul-Hyun; Bustamante, Carlos; Tinoco, Ignacio 2008 2008-01-11 PMC N PMC7094456 18021801.0 10.1016/j.jmb.2007.05.058 1fdpvswz 0.670782 Stork_2011, Guo_Y_2013, Pong_2011, Atkins_1999 Zhong_2016
19 Mazauric_2009 Interaction of the HIV-1 frameshift signal with the ribosome Mazauric, Marie-Hélène; Seol, Yeonee; Yoshizawa, Satoko; Visscher, Koen; Fourmy, Dominique 2009 2009-10-07 NONCOMM N PMC2794165 19812214.0 10.1093/nar/gkp779 ftxq9g7h 0.604138 Morikawa_1992, Brierley_1989, Atkins_1999, Guo_Y_2013, Stork_2011 Marcheschi_2007, Marczinke_1998
20 Larsen_1997 Structural probing and mutagenic analysis of the stem-loop required for Escherichia coli dnaX ribosomal frameshifting: programmed efficiency of 50% 1 1 Edited By D. E. Draper Larsen, Bente; Gesteland, Raymond F; Atkins, John F 1997 1997-08-08 PMC N PMC7126992 9300054.0 10.1006/jmbi.1997.1162 169j2woy 0.587748 Morikawa_1992, Hatfield_1990, Krause_1987, Brierley_1989 Marczinke_1998
21 Brierley_1991 Mutational analysis of the RNA pseudoknot component of a coronavirus ribosomal frameshifting signal Brierley, Ian; Rolley, Nicola J.; Jenner, Alison J.; Inglis, Stephen C. 1991 1991-08-20 PMC N PMC7131590 1880803.0 10.1016/0022-2836(91)90361-9 1m9s5bus 0.587145 Morikawa_1992, Brierley_1989, Hatfield_1990, Atkins_1999 Marczinke_1998
22 Goldsmith_2016 Selective Preference of Parallel DNA Triplexes Is Due to the Disruption of Hoogsteen Hydrogen Bonds Caused by the Severe Nonisostericity between the G*GC and T*AT Triplets Goldsmith, Gunaseelan; Rathinavelan, Thenmalarchelvi; Yathindra, Narayanarao 2016 2016-03-24 COMM-USE N PMC4807104 27010368.0 10.1371/journal.pone.0152102 tqx420oa 0.560680 Kierzek_2006, Guo_Y_2013, Brierley_1991 Cornish_2006
23 Vendeix_2012 Human tRNA(Lys3)(UUU) is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto-EnolTautomerism Vendeix, Franck A. P.; Murphy, Frank V.; Cantara, William A.; Leszczyńska, Grażyna; Gustilo, Estella M.; Sproat, Brian; Malkiewicz, Andrzej; Agris, Paul F. 2012 2012-03-01 PMC N PMC3662832 22227389.0 10.1016/j.jmb.2011.12.048 xx73wawr 0.527769 Morikawa_1992, Krause_1987, Powell_2011, Brierley_1989, Huang_2018 Tükenmez_2015, Marczinke_2000, Powell_2011
24 Chen_2017 Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot Chen, Yu-Ting; Chang, Kai-Chun; Hu, Hao-Teng; Chen, Yi-Lan; Lin, You-Hsin; Hsu, Chiung-Fang; Chang, Cheng-Fu; Chang, Kung-Yao; Wen, Jin-Der 2017 2017-06-02 None N PMC5449628 28334864.0 10.1093/nar/gkx134 aofirvc8 0.526506 Morikawa_1992, Brierley_1989, Atkins_1999, Brierley_1991 Marcheschi_2007, Cornish_2006, Marczinke_1998
25 Staple_2005 Pseudoknots: RNA Structures with Diverse Functions Staple, David W; Butcher, Samuel E 2005 2005-06-14 COMM-USE N PMC1149493 15941360.0 10.1371/journal.pbio.0030213 0brhn8oc 0.524483 Stork_2011, Gorbalenya_1988, Pleij_1994
26 Kai_Z_2019 An efficient simulated annealing algorithm for the RNA secondary structure prediction with Pseudoknots Kai, Zhang; Yuting, Wang; Yulin, Lv; Jun, Liu; Juanjuan, He 2019 2019-12-27 COMM-USE N PMC6933665 31881969.0 10.1186/s12864-019-6300-2 9z8z03rp 0.518096
27 Marcheschi_2007 Programmed Ribosomal Frameshifting in SIV is Induced by a Highly Structured RNA Stem-Loop Marcheschi, Ryan J.; Staple, David W.; Butcher, Samuel E. 2007 2007-10-01 PMC N PMC2080864 17868691.0 10.1016/j.jmb.2007.08.033 15s6otuz 0.513909 Pong_2011, Morikawa_1992, Stork_2011 Marczinke_1998
28 Shu-Yun_Le_1991 RNA pseudoknots downstream of the frameshift sites of retroviruses Shu-Yun Le, ; Shapiro, Bruce A.; Chen, Jih-H.; Nussinov, Ruth; Maizel, Jacob V. 1991 1991-11-30 PMC N 1663382.0 10.1016/1050-3862(91)90013-h i3bbo0qg 0.478364 Rice_1992, Ryu_W_2017, Pong_2011 Bhullar_2014
29 Chou_2009 An intermolecular RNA triplex provides insight into structural determinants for the pseudoknot stimulator of −1 ribosomal frameshifting Chou, Ming-Yuan; Chang, Kung-Yao 2009 2009-12-08 NONCOMM N PMC2836554 20007152.0 10.1093/nar/gkp1107 8gnn6l4b 0.447308 Morikawa_1992, Brierley_1989, Stork_2011, Atkins_1999, Brierley_1991 Su_M_2005, Marczinke_1998, Marcheschi_2007
30 Baril_2003 The Frameshift Stimulatory Signal of Human Immunodeficiency Virus Type 1 Group O is a Pseudoknot Baril, Martin; Dulude, Dominic; Steinberg, Sergey V; Brakier-Gingras, Léa 2003 2003-08-15 PMC N PMC7127721 12899829.0 10.1016/s0022-2836(03)00784-8 uftl1mx5 0.445783 Morikawa_1992, Jacks_1988, Hatfield_1990, Brierley_1989, Krause_1987 Marczinke_1998, Marcheschi_2007, Su_M_2005
31 Chen_2013 Dynamics of translation by single ribosomes through mRNA secondary structures Chen, Chunlai; Zhang, Haibo; Broitman, Steven L.; Reiche, Michael; Farrell, Ian; Cooperman, Barry S.; Goldman, Yale E. 2013 2013-03-31 None N PMC3648610 23542154.0 10.1038/nsmb.2544 l600aeuo 0.428011 Morikawa_1992, Huang_2018, Krause_1987 Balakin_1990
32 Kwak_2011 Annexin A2 Binds RNA and Reduces the Frameshifting Efficiency of Infectious Bronchitis Virus Kwak, Hoyun; Park, Min Woo; Jeong, Sunjoo 2011 2011-08-30 COMM-USE N PMC3168876 21918681.0 10.1371/journal.pone.0024067 uqrwq5qk 0.424551 Stork_2011, Pong_2011
33 Low_J_2014 Structure and Dynamics of the HIV-1 Frameshift Element RNA Low, Justin\nT.; Garcia-Miranda, Pablo; Mouzakis, Kathryn D.; Gorelick, Robert J.; Butcher, Samuel E.; Weeks, Kevin M. 2014 2014-06-13 PMC N PMC4089884 24926888.0 10.1021/bi5004926 y6qcig5u 0.422942 Morikawa_1992, Brierley_1989, Gorbalenya_1988, Krause_1987 Marcheschi_2007, Marczinke_1998
34 Cao_S_2008 Predicting ribosomal frameshifting efficiency Cao, Song; Chen, Shi-Jie 2008 2008-03-11 PMC N PMC2442619 18367782.0 10.1088/1478-3975/5/1/016002 5xqnpur7 0.408076 Morikawa_1992, Brierley_1989, Hatfield_1990, Huang_2018 Li_L_2001, Giedroc_2009
35 Chastain_1991 Structural Elements in RNA Chastain, Michael; Tinoco, Ignacio 1991 1991-12-31 PMC N 10.1016/s0079-6603(08)60008-2 4eu9v5d3 0.404915 Staple_2005, Liu_Y_2009, Martínez-Salas_2008 Kolchanov_1996
36 Pleij_1994 RNA pseudoknots Pleij, Cornelis W.A. 1994 1994-06-30 PMC N PMC7133496 10.1016/s0959-440x(94)90101-5 ai8n1oeq 0.402934 Staple_2005, Martínez-Salas_2008, Stork_2011 Xia_H_2015
37 Mouzakis_2012 HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome Mouzakis, Kathryn D.; Lang, Andrew L.; Vander Meulen, Kirk A.; Easterday, Preston D.; Butcher, Samuel E. 2012 2012-12-15 NONCOMM N PMC3561942 23248007.0 10.1093/nar/gks1254 ix8du1er 0.389890 Morikawa_1992, Brierley_1989, Hatfield_1990, Jacks_1988, Krause_1987 Marczinke_1998, Marcheschi_2007, Powell_2011
38 Kang_1998 Direct structural evidence for formation of a stem-loop structure involved in ribosomal frameshifting in human immunodeficiency virus type 1 1 Kumho Life and Environmental Science Laboratory Publication No. 8. 1 Kang, Hunseung 1998 1998-04-01 PMC N PMC7148724 9545540.0 10.1016/s0167-4781(98)00004-9 ppb9k3zu 0.386043 Morikawa_1992, Brierley_1989, Krause_1987, Firth_2009 Marczinke_1998, Marcheschi_2007
39 Väre_2017 Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function Väre, Ville Y. P.; Eruysal, Emily R.; Narendran, Amithi; Sarachan, Kathryn L.; Agris, Paul F. 2017 2017-03-16 COMM-USE N PMC5372741 28300792.0 10.3390/biom7010029 xva1qkrd 0.383667 Staple_2005, Martínez-Salas_2008, Stork_2011 Byszewska_2015, Kolchanov_1996
40 Yu_C_2010 Stimulation of ribosomal frameshifting by antisense LNA Yu, Chien-Hung; Noteborn, Mathieu H. M.; Olsthoorn, René C. L. 2010 2010-08-06 NONCOMM N PMC3001050 20693527.0 10.1093/nar/gkq650 pc4x5e24 0.381950 Morikawa_1992, Stork_2011, Brierley_1989, Krause_1987 Marcheschi_2007
41 Ishimaru_2012 RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus Ishimaru, Daniella; Plant, Ewan P.; Sims, Amy C.; Yount, Boyd L.; Roth, Braden M.; Eldho, Nadukkudy V.; Pérez-Alvarado, Gabriela C.; Armbruster, David W.; Baric, Ralph S.; Dinman, Jonathan D.; Taylor, Deborah R.; Hennig, Mirko 2012 2012-12-26 NONCOMM N PMC3575852 23275571.0 10.1093/nar/gks1361 zrbn637z 0.353117 Stork_2011, Pong_2011, Morikawa_1992, Lin_X_2015 Su_M_2005, Xia_H_2015
42 Atkins_1999 Intricacies of ribosomal frameshifting Atkins, John F.; Gesteland, Raymond F. 1999 1999-01-01 PMC N PMC7096882 10074934.0 10.1038/6642 14iqq6wy 0.346499 Morikawa_1992, Lamb_1991, Hatfield_1990, Brierley_1989 Trifonov_1992, Gopinath_2015, Hatfield_1990
43 de Messieres_2014 Single-Molecule Measurements of the CCR5 mRNA Unfolding Pathways de Messieres, Michel; Chang, Jen-Chien; Belew, Ashton Trey; Meskauskas, Arturas; Dinman, Jonathan D.; La Porta, Arthur 2014 2014-01-01 PMC N PMC3907219 24411256.0 10.1016/j.bpj.2013.09.036 dvnkhgov 0.341850 Morikawa_1992, Brierley_1989, Hatfield_1990, Atkins_1999, Martínez-Salas_2008 Bénard_1996
44 Su_M_2005 An atypical RNA pseudoknot stimulator and an upstream attenuation signal for −1 ribosomal frameshifting of SARS coronavirus Su, Mei-Chi; Chang, Chung-Te; Chu, Chiu-Hui; Tsai, Ching-Hsiu; Chang, Kung-Yao 2005 2005-07-29 PMC N PMC1182165 16055920.0 10.1093/nar/gki731 7ots8npg 0.335670 Morikawa_1992, Brierley_1989, Stork_2011, Jacks_1988, Pong_2011 Marczinke_1998, Li_L_2001
45 Lee_C_2011 The solution structure of coronaviral stem-loop 2 (SL2) reveals a canonical CUYG tetraloop fold Lee, Chul Won; Li, Lichun; Giedroc, David P. 2011 2011-04-06 PMC N PMC3086565 21382373.0 10.1016/j.febslet.2011.03.002 ehwdg722 0.332966 Pong_2011, Morikawa_1992, Gorbalenya_1988, Lin_X_2015 Li_L_2008
46 Park_2008 Identification of novel ligands for the RNA pseudoknot that regulate −1 ribosomal frameshifting Park, So-Jung; Jung, Young Hoon; Kim, Yang-Gyun; Park, Hyun-Ju 2008 2008-04-15 PMC N PMC7125880 18321712.0 10.1016/j.bmc.2008.02.025 a0r9q8ms 0.322995 Stork_2011, Pong_2011, Rice_1992 Xia_H_2015
47 Chang_2012 Revealing −1 Programmed Ribosomal Frameshifting Mechanisms by Single-Molecule Techniques and Computational Methods Chang, Kai-Chun 2012 2012-04-01 COMM-USE N PMC3321566 22545064.0 10.1155/2012/569870 ne7rvqex 0.310890 Martínez-Salas_2008, Wu_B_2009, Stork_2011 Zhong_2016, Marcheschi_2007