Topic 06 -- Abstracts with Biological Entities (English) - 75 Topics / Sub-Topic Model 55 - 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 Li_C_2016 Conformational Flexibility of a Short Loop near the Active Site of the SARS-3CLpro is Essential to Maintain Catalytic Activity Li, Chunmei; Teng, Xin; Qi, Yifei; Tang, Bo; Shi, Hailing; Ma, Xiaomin; Lai, Luhua 2016 2016-02-16 COMM-USE N PMC4754693 26879383.0 10.1038/srep20918 n69iewmx 0.969180 Someya_2008, Kanitz_2019, Wei_P_2006, Hu_T_2009
2 Chen_2010 Liberation of SARS-CoV main protease from the viral polyprotein: N-terminal autocleavage does not depend on the mature dimerization mode Chen, Shuai; Jonas, Felix; Shen, Can; Higenfeld, Rolf 2010 2010-01-01 PMC N PMC4875104 21203998.0 10.1007/s13238-010-0011-4 6kkzh1tp 0.892804 Yang_2010 Piñón_1997
3 Zhong_2009 C-terminal domain of SARS-CoV main protease can form a 3D domain-swapped dimer Zhong, Nan; Zhang, Shengnan; Xue, Fei; Kang, Xue; Zou, Peng; Chen, Jiaxuan; Liang, Chao; Rao, Zihe; Jin, Changwen; Lou, Zhiyong; Xia, Bin 2009 2009-01-01 PMC N PMC2762595 19319935.0 10.1002/pro.76 3xc9y5mo 0.822553 Sato_2019 Tsai_2010
4 Lim_L_2014 Dynamically-Driven Enhancement of the Catalytic Machinery of the SARS 3C-Like Protease by the S284-T285-I286/A Mutations on the Extra Domain Lim, Liangzhong; Shi, Jiahai; Mu, Yuguang; Song, Jianxing 2014 2014-07-18 COMM-USE N PMC4103764 25036652.0 10.1371/journal.pone.0101941 u9zazctj 0.821035 Someya_2008, Shi_J_2011, Kanitz_2019, Buller_2012
5 Shi_J_2011 Dynamically-Driven Inactivation of the Catalytic Machinery of the SARS 3C-Like Protease by the N214A Mutation on the Extra Domain Shi, Jiahai; Han, Nanyu; Lim, Liangzhong; Lua, Shixiong; Sivaraman, J.; Wang, Lushan; Mu, Yuguang; Song, Jianxing 2011 2011-02-24 COMM-USE N PMC3044768 21390281.0 10.1371/journal.pcbi.1001084 2beyphz7 0.802340 Someya_2008, Piñón_1997, Kanitz_2019, Cheng_2010
6 Shi_J_2006 The catalysis of the SARS 3C‐like protease is under extensive regulation by its extra domain Shi, Jiahai; Song, Jianxing 2006 2006-02-08 PMC N PMC7164011 16478476.0 10.1111/j.1742-4658.2006.05130.x w00rcvd8 0.739967
7 Zheng_2006 Insight into the activity of SARS main protease: Molecular dynamics study of dimeric and monomeric form of enzyme Zheng, Kewen; Ma, Guozheng; Zhou, Jinming; Zen, Min; Zhao, Wenna; Jiang, Yongjun; Yu, Qingsen; Feng, Jialiang 2006 2006-11-02 PMC N PMC7167853 17083088.0 10.1002/prot.21160 d2algx16 0.734523
8 Zhang_2010 Three-dimensional domain swapping as a mechanism to lock the active conformation in a super-active octamer of SARS-CoV main protease Zhang, Shengnan; Zhong, Nan; Xue, Fei; Kang, Xue; Ren, Xiaobai; Chen, Jiaxuan; Jin, Changwen; Lou, Zhiyong; Xia, Bin 2010 2010-04-01 PMC N PMC4875095 21203949.0 10.1007/s13238-010-0044-8 gdmp0re0 0.723029 Zhong_2009, Lee_T_2007, Kanitz_2019, Tsai_2010
9 Lim_L_2019 Structurally- and dynamically-driven allostery of the chymotrypsin-like proteases of SARS, Dengue and Zika viruses Lim, Liangzhong; Gupta, Garvita; Roy, Amrita; Kang, Jian; Srivastava, Shagun; Shi, Jiahai; Song, Jianxing 2019 2019-05-31 PMC N PMC7111307 30217495.0 10.1016/j.pbiomolbio.2018.08.009 3aydbdmu 0.704013 Vaughan_2012 Tsai_2010, Someya_2008, Yu_L_2017
10 Tsai_2010 Essential covalent linkage between the chymotrypsin-like domain and the extra domain of the SARS-CoV main protease Tsai, Meng-Ying; Chang, Wei-Hsin; Liang, Jin-Yi; Lin, Long-Liu; Chang, Gu-Gang; Chang, Hui-Ping 2010 2010-08-28 PMC N PMC7110190 20587646.0 10.1093/jb/mvq071 w2q5468y 0.701332 Sato_2019 Piñón_1997
11 Zhang_2010 (1)H, (13)C and (15)N resonance assignments of SARS-CoV main protease N-terminal domain Zhang, Shengnan; Zhong, Nan; Ren, Xiaobai; Jin, Changwen; Xia, Bin 2010 2010-12-23 PMC N PMC7091140 21181312.0 10.1007/s12104-010-9287-9 iy57tjx5 0.626490 Yang_2010 Zhong_2009, Lee_T_2007
12 Guy_J_2005 Identification of critical active‐site residues in angiotensin‐converting enzyme‐2 (ACE2) by site‐directed mutagenesis Guy, Jodie L.; Jackson, Richard M.; Jensen, Hanne A.; Hooper, Nigel M.; Turner, Anthony J. 2005 2005-07-19 PMC N PMC7164114 16008552.0 10.1111/j.1742-4658.2005.04756.x hext9jv8 0.592836
13 Ho_B_2015 Critical Assessment of the Important Residues Involved in the Dimerization and Catalysis of MERS Coronavirus Main Protease Ho, Bo-Lin; Cheng, Shu-Chun; Shi, Lin; Wang, Ting-Yun; Ho, Kuan-I; Chou, Chi-Yuan 2015 2015-12-14 COMM-USE N PMC4682845 26658006.0 10.1371/journal.pone.0144865 ipi81ce3 0.588588 Lin_M_2014
14 Aeksiri_2017 Structural insights into type I and type II of nsp4 porcine reproductive and respiratory syndrome virus (nsp4 PRRSV) by molecular dynamics simulations Aeksiri, Niran; Jantafong, Tippawan 2017 2017-06-30 PMC N PMC7110526 28411461.0 10.1016/j.jmgm.2017.03.015 wsd30c6f 0.587777
15 Lin_M_2014 Structural and functional characterization of MERS coronavirus papain-like protease Lin, Min-Han; Chuang, Shang-Ju; Chen, Chiao-Che; Cheng, Shu-Chun; Cheng, Kai-Wen; Lin, Chao-Hsiung; Sun, Chiao-Yin; Chou, Chi-Yuan 2014 2014-06-04 COMM-USE N PMC4051379 24898546.0 10.1186/1423-0127-21-54 fb04slz0 0.576586 Yu_L_2017
16 Chen_2008 Residues on the Dimer Interface of SARS Coronavirus 3C-like Protease: Dimer Stability Characterization and Enzyme Catalytic Activity Analysis Chen, Shuai; Zhang, Jian; Hu, Tiancen; Chen, Kaixian; Jiang, Hualiang; Shen, Xu 2008 2008-01-07 PMC N PMC7109808 18182387.0 10.1093/jb/mvm246 m6iocvo7 0.559010 Wei_P_2006, Hu_T_2009, Someya_2008, Kanitz_2019
17 ZHOU_2008 A cysteine-rich metal-binding domain from rubella virus non-structural protein is essential for viral protease activity and virus replication ZHOU, Yubin; TZENG, Wen-Pin; YE, Yiming; HUANG, Yun; LI, Shunyi; CHEN, Yanyi; FREY, Teryl K.; YANG, Jenny J. 2008 2008-12-23 PMC N PMC2908387 18795894.0 10.1042/bj20081468 z7z7sf7b 0.515378 Yang_2010
18 Cheng_2010 Mutation of Glu-166 Blocks the Substrate-Induced Dimerization of SARS Coronavirus Main Protease Cheng, Shu-Chun; Chang, Gu-Gang; Chou, Chi-Yuan 2010 2010-04-07 None N PMC2849084 20371333.0 10.1016/j.bpj.2009.12.4272 xrb8zibf 0.507143 Sato_2019 Wei_P_2006, Someya_2008, van_der_Linden_2014
19 Wu_C_2013 Mechanism for controlling the monomer–dimer conversion of SARS coronavirus main protease Wu, Cheng‐Guo; Cheng, Shu‐Chun; Chen, Shiang‐Chuan; Li, Juo‐Yan; Fang, Yi‐Hsuan; Chen, Yau‐Hung; Chou, Chi‐Yuan 2013 2013-05-01 PMC N PMC7161611 23633583.0 10.1107/s0907444913001315 baqlezoj 0.496192 Sato_2019
20 Phakthanakanok_2009 A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism Phakthanakanok, Krongsakda; Ratanakhanokchai, Khanok; Kyu, Khin Lay; Sompornpisut, Pornthep; Watts, Aaron; Pinitglang, Surapong 2009 2009-01-30 COMM-USE N PMC2648740 19208150.0 10.1186/1471-2105-10-s1-s48 8necodtw 0.482480 Wei_P_2006, Zhu_L_2011, Niu_C_2008, Lee_T_2007
21 Wei_P_2006 The N-terminal octapeptide acts as a dimerization inhibitor of SARS coronavirus 3C-like proteinase Wei, Ping; Fan, Keqiang; Chen, Hao; Ma, Liang; Huang, Changkang; Tan, Lei; Xi, Dong; Li, Chunmei; Liu, Ying; Cao, Aoneng; Lai, Luhua 2006 2006-01-20 PMC N PMC7092940 16329994.0 10.1016/j.bbrc.2005.11.102 67brxejx 0.468783 Yang_2010 Cheng_2010, van_der_Linden_2014, Someya_2008
22 Lei_J_2016 Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin Lei, Jian; Hilgenfeld, Rolf 2016 2016-05-30 PMC N PMC7090527 27245450.0 10.1007/s12250-016-3742-4 4cgrjnjo 0.451897 Sato_2019
23 Hu_T_2009 Two adjacent mutations on the dimer interface of SARS coronavirus 3C-like protease cause different conformational changes in crystal structure Hu, Tiancen; Zhang, Yu; Li, Lianwei; Wang, Kuifeng; Chen, Shuai; Chen, Jing; Ding, Jianping; Jiang, Hualiang; Shen, Xu 2009 2009-06-05 PMC N PMC7103376 19409595.0 10.1016/j.virol.2009.03.034 qk8g4c7e 0.450618 Someya_2008, Chen_2008, Wei_P_2006, Cheng_2010
24 Guan_2010 Structures of two elapid snake venom metalloproteases with distinct activities highlight the disulfide patterns in the D domain of ADAMalysin family proteins Guan, Hong-Hsiang; Goh, King-Siang; Davamani, Fabian; Wu, Po-Long; Huang, Yen-Wei; Jeyakanthan, Jeyaraman; Wu, Wen-guey; Chen, Chun-Jung 2010 2010-03-31 PMC N PMC7129284 19932752.0 10.1016/j.jsb.2009.11.009 rwqo6b8x 0.449600 Tsai_2010
25 Chou_2012 Differential domain structure stability of the severe acute respiratory syndrome coronavirus papain-like protease Chou, Ya-Wen; Cheng, Shu-Chun; Lai, Hsing-Yi; Chou, Chi-Yuan 2012 2012-04-15 None N PMC7094420 22391227.0 10.1016/j.abb.2012.02.015 px6dfzz4 0.436435 Yu_L_2017, Tsai_2010
26 Barrila_2006 Long Range Cooperative Interactions Modulate Dimerization in SARS 3CL(pro) Barrila, Jennifer; Bacha, Usman; Freire, Ernesto 2006 2006-12-01 PMC N PMC2570436 17154528.0 10.1021/bi0616302 fxz80tr1 0.331026 Vaughan_2012 Wei_P_2006, Cheng_2010, Barrila_2010
27 Anand_2002 Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra α-helical domain Anand, Kanchan; Palm, Gottfried J.; Mesters, Jeroen R.; Siddell, Stuart G.; Ziebuhr, John; Hilgenfeld, Rolf 2002 2002-07-01 PMC N PMC126080 12093723.0 10.1093/emboj/cdf327 2sfqsfm1 0.330605 Sato_2019 Piñón_1997, Tsai_2010, Rozanov_1995
28 Xia_B_2011 Activation and maturation of SARS-CoV main protease Xia, Bin; Kang, Xue 2011 2011-04-01 PMC N PMC4875205 21533772.0 10.1007/s13238-011-1034-1 0oh701o3 0.324597
29 Hilgenfeld_2014 From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design Hilgenfeld, Rolf 2014 2014-08-11 PMC N PMC7163996 25039866.0 10.1111/febs.12936 ac6m1uwp 0.324002
30 Thangapandian_2012 Structural Origins for the Loss of Catalytic Activities of Bifunctional Human LTA4H Revealed through Molecular Dynamics Simulations Thangapandian, Sundarapandian; John, Shalini; Lazar, Prettina; Choi, Sun; Lee, Keun Woo 2012 2012-07-25 COMM-USE N PMC3405069 22848428.0 10.1371/journal.pone.0041063 w9iwmqgq 0.323461 Buller_2012, Someya_2008, Kanitz_2019, Yin_J_2007
31 Barrila_2010 Mutation of Asn28 disrupts the dimerization and enzymatic activity of SARS 3CL(pro) Barrila, Jennifer; Gabelli, Sandra B.; Bacha, Usman; Amzel, L. Mario; Freire, Ernesto 2010 2010-05-25 PMC N PMC2877132 20420403.0 10.1021/bi1002585 iccni6od 0.313476 Wei_P_2006, Barrila_2006, Cheng_2010