Topic 12 -- 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 Kieft_2020 Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes Kieft, Rudo; Zhang, Yang; Marand, Alexandre P.; Moran, Jose Dagoberto; Bridger, Robert; Wells, Lance; Schmitz, Robert J.; Sabatini, Robert 2020 2020-02-21 COMM-USE N PMC7055916 32084124.0 10.1371/journal.pgen.1008390 h2xdkoyq 0.932338 Stork_2011 Kieft_2019
2 Kim_H_2019 RNA-Dependent RNA Polymerase Speed and Fidelity are not the Only Determinants of the Mechanism or Efficiency of Recombination Kim, Hyejeong; Ellis, Victor D.; Woodman, Andrew; Zhao, Yan; Arnold, Jamie J.; Cameron, Craig E. 2019 2019-11-25 COMM-USE N PMC6947342 31775299.0 10.3390/genes10120968 vbmkasx2 0.839965 Stork_2011, Masante_2015 Kim_H_2019
3 Kim_H_2019 RNA-dependent RNA polymerase speed and fidelity are not the only determinants of the mechanism or efficiency of recombination Hyejeong Kim; Victor D. Ellis; Andrew Woodman; Yan Zhao; Jamie J. Arnold; Craig E. Cameron 2019 2019-09-14 BioRxiv N 10.1101/769224 ljz7rfny 0.827805 Stork_2011 Kim_H_2019
4 Wijngaert_2020 Cryo-EM structures reveal transcription initiation steps by yeast mitochondrial RNA polymerase Brent De Wijngaert; Shemaila Sultana; Chhaya Dharia; Hans Vanbuel; Jiayu Shen; Daniel vasilchuk; Sergio E Martinez; Eaazhisai Kandiah; Smita S Patel; Kalyan Das 2020 2020-04-14 BioRxiv N 10.1101/2020.04.13.038620 ex3zlq38 0.827654 Stork_2011, Herold_2001, Pong_2011 Bhullar_2014
5 Kieft_2019 Identification of a Novel Base J Binding Protein Complex Involved in RNA Polymerase II Transcription Termination in Trypanosomes Rudo Kieft; Yang Zhang; Alexandre P. Marand; Jose Dagoberto Moran; Robert Bridger; Lance Wells; Robert J. Schmitz; Robert Sabatini 2019 2019-08-30 BioRxiv N 10.1101/753004 j3u7yq3y 0.823459 Stork_2011 Kieft_2020
6 Otsuka_1999 Similarity relations of DNA and RNA polymerases investigated by the principal component analysis of amino acid sequences Otsuka, Jinya; Kikuchi, Norihiro; Kojima, Shinji 1999 1999-10-12 PMC N 10525143.0 10.1016/s0167-4838(99)00187-9 4z5jxxf2 0.795265 Gorbalenya_1988, Stork_2011, Payne_2017 Nowak_1984
7 Achuthan_2015 Alternative divalent cations (Zn(2+), Co(2+), and Mn(2+)) are not mutagenic at conditions optimal for HIV-1 reverse transcriptase activity Achuthan, Vasudevan; DeStefano, Jeffrey J 2015 2015-05-03 COMM-USE N PMC4472245 25934642.0 10.1186/s12858-015-0041-x iexd5qn5 0.772714 Stork_2011
8 Liu_X_2015 Nucleobase but not Sugar Fidelity is Maintained in the Sabin I RNA-Dependent RNA Polymerase Liu, Xinran; Musser, Derek M.; Lee, Cheri A.; Yang, Xiaorong; Arnold, Jamie J.; Cameron, Craig E.; Boehr, David D. 2015 2015-10-26 COMM-USE N PMC4632402 26516899.0 10.3390/v7102894 o43cfrfh 0.756273 Stork_2011, Rice_1992
9 te_Velthuis_2011 The SARS-coronavirus nsp7+nsp8 complex is a unique multimeric RNA polymerase capable of both de novo initiation and primer extension te Velthuis, Aartjan J.W.; van den Worm, Sjoerd H. E.; Snijder, Eric J. 2011 2011-10-29 NONCOMM N PMC3287201 22039154.0 10.1093/nar/gkr893 tx0lqgff 0.712967 Stork_2011, Pong_2011 Ahn_D_2012
10 Ju_J_2020 Nucleotide Analogues as Inhibitors of SARS-CoV Polymerase Jingyue Ju; Xiaoxu Li; Shiv Kumar; Steffen Jockusch; Minchen Chien; Chuanjuan Tao; Irina Morozova; Sergey Kalachikov; Robert N. Kirchdoerfer; James J. Russo 2020 2020-03-14 BioRxiv Y 10.1101/2020.03.12.989186 hj675z1b 0.705534 Stork_2011, Pong_2011
11 Freistadt_2007 Conserved aspartic acid 233 and alanine 231 are not required for poliovirus polymerase function in replicons Freistadt, Marion S; Eberle, Karen E 2007 2007-03-12 COMM-USE N PMC1839082 17352827.0 10.1186/1743-422x-4-28 y6mp3rk9 0.675803 Gorbalenya_1988, Stork_2011 Gopinath_2015, Xia_H_2015
12 Wehrfritz_2007 Reconstitution of bluetongue virus polymerase activity from isolated domains based on a three‐dimensional structural model Wehrfritz, Josa‐marie; Boyce, Mark; Mirza, Sahdia; Roy, Polly 2007 2007-02-23 PMC N PMC7161780 17323325.0 10.1002/bip.20706 nb4uryxk 0.674472 Stork_2011, Pong_2011, Gorbalenya_1988
13 Zhang_2005 De novo RNA synthesis and homology modeling of the classical swine fever virus RNA polymerase Zhang, Pengwei; Xie, Jian; Yi, Guanghui; Zhang, Chuyu; Zhou, Rong 2005 2005-09-30 PMC N PMC7126667 16022897.0 10.1016/j.virusres.2005.03.003 13h5aigg 0.665400 Pong_2011, Stork_2011, Gorbalenya_1988 Tzeng_2006, Zhou_2011, Potisopon_2014
14 Lehmann_2016 Arterivirus RNA-dependent RNA polymerase: Vital enzymatic activity remains elusive Lehmann, Kathleen C.; Gorbalenya, Alexander E.; Snijder, Eric J.; Posthuma, Clara C. 2016 2016-01-31 PMC N PMC7111705 26499043.0 10.1016/j.virol.2015.10.002 xzw8iwzf 0.655723 Stork_2011, Pong_2011, Rice_1992 Yu_F_2007
15 Yu_F_2007 Identification and characterization of RNA-dependent RNA polymerase activity in recombinant Japanese encephalitis virus NS5 protein Yu, F.; Hasebe, F.; Inoue, S.; Mathenge, E. G. M.; Morita, K. 2007 2007-06-18 PMC N PMC7086876 17577613.0 10.1007/s00705-007-1007-0 s0lcyjgh 0.604384 Stork_2011, Pong_2011, Rice_1992 Tzeng_2006, Nowak_1984
16 Tonzi_2018 Translesion polymerase kappa-dependent DNA synthesis underlies replication fork recovery Tonzi, Peter; Yin, Yandong; Lee, Chelsea Wei Ting; Rothenberg, Eli; Huang, Tony T 2018 2018-11-13 COMM-USE N PMC6251625 30422114.0 10.7554/elife.41426 ivl1e9vd 0.576831 Stork_2011 Sasvari_2011
17 Moustafa_2011 Molecular Dynamics Simulations of Viral RNA Polymerases Link Conserved and Correlated Motions of Functional Elements to Fidelity Moustafa, Ibrahim M.; Shen, Hujun; Morton, Brandon; Colina, Coray M.; Cameron, Craig E. 2011 2011-07-01 None N PMC3114172 21575642.0 10.1016/j.jmb.2011.04.078 f25vti5y 0.565271 Stork_2011, Pong_2011, Lin_X_2015, Rice_1992 YU_W_1995, Zhou_2011
18 Liu_W_2018 A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase Liu, Weichi; Shi, Xiaoling; Gong, Peng 2018 2018-11-16 COMM-USE N PMC6237809 30239956.0 10.1093/nar/gky848 ya0siivm 0.562531 Stork_2011, Pong_2011
19 Cameron_2009 Dynamics: the missing link between structure and function of the viral RNA-dependent RNA polymerase? Cameron, Craig E; Moustafa, Ibrahim M; Arnold, Jamie J 2009 2009-12-31 PMC N 19910183.0 10.1016/j.sbi.2009.10.012 fm44fqqb 0.549701 Stork_2011, Wu_B_2009
20 Ahn_D_2012 Biochemical characterization of a recombinant SARS coronavirus nsp12 RNA-dependent RNA polymerase capable of copying viral RNA templates Ahn, Dae-Gyun; Choi, Jin-Kyu; Taylor, Deborah R.; Oh, Jong-Won 2012 2012-07-13 PMC N PMC7086750 22791111.0 10.1007/s00705-012-1404-x 1tlxfc6r 0.548829 Stork_2011, Pong_2011, Rice_1992 Tzeng_2006
21 Imbert_2006 A second, non-canonical RNA-dependent RNA polymerase in SARS Coronavirus Imbert, Isabelle; Guillemot, Jean-Claude; Bourhis, Jean-Marie; Bussetta, Cécile; Coutard, Bruno; Egloff, Marie-Pierre; Ferron, François; Gorbalenya, Alexander E; Canard, Bruno 2006 2006-10-05 PMC N PMC1618104 17024178.0 10.1038/sj.emboj.7601368 31by8zse 0.545222 Stork_2011, Pong_2011, Gorbalenya_1988 Ahn_D_2012, Bhullar_2014
22 Ghorai_2010 Molecular characterization of genome segment 2 encoding RNA dependent RNA polymerase of Antheraea mylitta cytoplasmic polyhedrosis virus Ghorai, Suvankar; Chakrabarti, Mrinmay; Roy, Sobhan; Chavali, Venkata Ramana Murthy; Bagchi, Abhisek; Ghosh, Ananta Kumar 2010 2010-08-15 PMC N PMC7111928 20488502.0 10.1016/j.virol.2010.04.019 bd2bkz5t 0.540984 Wurch_1991, Luytjes_1988, Gorbalenya_1988, Stork_2011 Goldberg_1991, Nowak_1984, Tzeng_2006
23 Nirwan_2019 Chapter 11 Rhinovirus RNA Polymerase Structure, Function, and Inhibitors Nirwan, Sonam; Kakkar, Rita 2019 2019-12-31 PMC N 10.1016/b978-0-12-815422-9.00011-5 qx0qdjmt 0.524641 Stork_2011, Pong_2011, Rice_1992, Lin_X_2015, Payne_2017
24 Gorbalenya_2002 The Palm Subdomain-based Active Site is Internally Permuted in Viral RNA-dependent RNA Polymerases of an Ancient Lineage Gorbalenya, Alexander E; Pringle, Fiona M; Zeddam, Jean-Louis; Luke, Brian T; Cameron, Craig E; Kalmakoff, James; Hanzlik, Terry N; Gordon, Karl H.J; Ward, Vernon K 2002 2002-11-15 PMC N PMC7127740 12421558.0 10.1016/s0022-2836(02)01033-1 468kk47s 0.511910 Gorbalenya_1988, Pong_2011, Stork_2011, Morikawa_1992, Imbert_2006 Xia_H_2015
25 Potisopon_2014 The methyltransferase domain of dengue virus protein NS5 ensures efficient RNA synthesis initiation and elongation by the polymerase domain Potisopon, Supanee; Priet, Stéphane; Collet, Axelle; Decroly, Etienne; Canard, Bruno; Selisko, Barbara 2014 2014-10-13 COMM-USE N PMC4191377 25209234.0 10.1093/nar/gku666 jhn81kon 0.510179 Stork_2011, Pong_2011 Bhullar_2014, Sasvari_2011
26 te_Velthuis_2009 The RNA polymerase activity of SARS-coronavirus nsp12 is primer dependent te Velthuis, Aartjan J. W.; Arnold, Jamie J.; Cameron, Craig E.; van den Worm, Sjoerd H. E.; Snijder, Eric J. 2009 2009-10-29 NONCOMM N PMC2800238 19875418.0 10.1093/nar/gkp904 oa24d6ic 0.474505 Stork_2011, Pong_2011, Rice_1992 Ahn_D_2012
27 Sarnowska_2007 Hairpin structure within the 3′UTR of DNA polymerase β mRNA acts as a post-transcriptional regulatory element and interacts with Hax-1 Sarnowska, Elżbieta; Grzybowska, Ewa A.; Sobczak, Krzysztof; Konopiński, Ryszard; Wilczyńska, Anna; Szwarc, Maria; Sarnowski, Tomasz J.; Krzyżosiak, Włodzimierz J.; Siedlecki, Janusz A. 2007 2007-08-17 NONCOMM N PMC2018635 17704138.0 10.1093/nar/gkm502 l92nlegt 0.473324
28 Tchesnokov_2019 Mechanism of Inhibition of Ebola Virus RNA-Dependent RNA Polymerase by Remdesivir Tchesnokov, Egor P.; Feng, Joy Y.; Porter, Danielle P.; Götte, Matthias 2019 2019-04-04 COMM-USE N PMC6520719 30987343.0 10.3390/v11040326 rn3bjc9d 0.466193 Stork_2011, Pong_2011, Masante_2015
29 Mishra_2014 Unfolding of in planta activity of anti‐rep ribozyme in presence of a RNA silencing suppressor Mishra, Sumona Karjee; Chilakamarthi, Ushasri; Deb, J.K.; Mukherjee, Sunil Kumar 2014 2014-05-21 PMC N PMC7164126 24735726.0 10.1016/j.febslet.2014.04.006 pa65xxt2 0.437210 Stork_2011, Pong_2011, Landeo-Ríos_2016
30 Selisko_2018 Structural and Functional Basis of the Fidelity of Nucleotide Selection by Flavivirus RNA-Dependent RNA Polymerases Selisko, Barbara; Papageorgiou, Nicolas; Ferron, François; Canard, Bruno 2018 2018-01-30 COMM-USE N PMC5850366 29385764.0 10.3390/v10020059 e993uavn 0.429234 Stork_2011, Rice_1992, Payne_2017, Gorbalenya_1988 Zhou_2011, Masante_2015
31 Lin_X_2015 Subgenomic promoter recognition by the norovirus RNA-dependent RNA polymerases Lin, Xiaoyan; Thorne, Lucy; Jin, Zhinan; Hammad, Loubna A.; Li, Serena; Deval, Jerome; Goodfellow, Ian G.; Kao, C. Cheng 2015 2015-01-09 COMM-USE N PMC4288183 25520198.0 10.1093/nar/gku1292 v3sfww3e 0.418137 Stork_2011, Rice_1992, Pong_2011, Banerjee_2001 Bhullar_2014
32 Yin_W_2020 Structural Basis for the Inhibition of the RNA-Dependent RNA Polymerase from SARS-CoV-2 by Remdesivir Wanchao Yin; Chunyou Mao; Xiaodong Luan; Dan-Dan Shen; Qingya Shen; Haixia Su; Xiaoxi Wang; Fulai Zhou; Wenfeng Zhao; Minqi Gao; Shenghai Chang; Yuan-Chao Xie; Guanghui Tian; He-Wei Jiang; Sheng-Ce Tao; Jingshan Shen; Yi Jiang; Hualiang Jiang; Yechun Xu; Shuyang Zhang; Yan Zhang; H. Eric Xu 2020 2020-04-09 BioRxiv Y 10.1101/2020.04.08.032763 7v7pzclb 0.417700 Stork_2011, Pong_2011, Lin_X_2015 Ahn_D_2012
33 Jia_H_2019 A Structure-Function Diversity Survey of the RNA-Dependent RNA Polymerases From the Positive-Strand RNA Viruses Jia, Hengxia; Gong, Peng 2019 2019-08-22 COMM-USE N PMC6713929 31507560.0 10.3389/fmicb.2019.01945 0bnfugdm 0.400699 Gorbalenya_1988, Stork_2011, Rice_1992, Pong_2011, Payne_2017 Zhou_2011, Xia_H_2015
34 Zhou_2011 Mutational analysis of the SDD sequence motif of a PRRSV RNA-dependent RNA polymerase Zhou, Yan; Zheng, HaiHong; Gao, Fei; Tian, DeBin; Yuan, ShiShan 2011 2011-09-16 NONCOMM N PMC7088696 21922433.0 10.1007/s11427-011-4216-4 yo9libo0 0.382100 Stork_2011, Rice_1992, Pong_2011 Masante_2015, Tzeng_2006
35 Penno_2017 Stimulation of reverse transcriptase generated cDNAs with specific indels by template RNA structure: retrotransposon, dNTP balance, RT-reagent usage Penno, Christophe; Kumari, Romika; Baranov, Pavel V.; van Sinderen, Douwe; Atkins, John F. 2017 2017-09-29 NONCOMM N PMC5737552 28973469.0 10.1093/nar/gkx689 k4gtl2o7 0.358905 Stork_2011, Morikawa_1992, Lamb_1991, Rice_1992, Payne_2017
36 Woodman_2016 Biochemical and genetic analysis of the role of the viral polymerase in enterovirus recombination Woodman, Andrew; Arnold, Jamie J.; Cameron, Craig E.; Evans, David J. 2016 2016-08-19 COMM-USE N PMC5001610 27317698.0 10.1093/nar/gkw567 6o70ybpf 0.355612 Rice_1992, Stork_2011, Masante_2015 Nowak_1984, Adams_2003
37 Castro_2005 Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective Castro, Christian; Arnold, Jamie J.; Cameron, Craig E. 2005 2005-02-28 PMC N PMC7125856 15649560.0 10.1016/j.virusres.2004.11.004 9c8dj9j7 0.336478 Stork_2011, Rice_1992, Payne_2017, Lin_X_2015 Bhullar_2014
38 Posthuma_2017 Nidovirus RNA polymerases: Complex enzymes handling exceptional RNA genomes Posthuma, Clara C.; te Velthuis, Aartjan J.W.; Snijder, Eric J. 2017 2017-04-15 PMC N PMC7114556 28174054.0 10.1016/j.virusres.2017.01.023 g4sg2nex 0.333009 Rice_1992, Stork_2011, Pong_2011 Xia_H_2015
39 Beerens_2007 De Novo Initiation of RNA Synthesis by the Arterivirus RNA-Dependent RNA Polymerase Beerens, Nancy; Selisko, Barbara; Ricagno, Stefano; Imbert, Isabelle; van der Zanden, Linda; Snijder, Eric J.; Canard, Bruno 2007 2007-05-30 None N PMC1951334 17537850.0 10.1128/jvi.00564-07 7g1lrzcj 0.305821 Stork_2011, Rice_1992 Tzeng_2006
40 Lang_2012 Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases Lang, Dorothy M.; Zemla, A. T.; Zhou, C. L. Ecale 2012 2012-12-25 NONCOMM N PMC3561941 23275546.0 10.1093/nar/gks1251 s90geszi 0.300507 Gorbalenya_1988, Staple_2005, Payne_2017, Rice_1992