Topic 11 -- Abstracts with Biological Entities (English) - 75 Topics / Sub-Topic Model 10 - 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 Chien_2013 Assembling an ion channel: ORF 3a from SARS‐CoV Chien, Tze‐Hsiang; Chiang, Ya‐Ling; Chen, Chin‐Pei; Henklein, Petra; Hänel, Karen; Hwang, Ing‐Shouh; Willbold, Dieter; Fischer, Wolfgang B. 2013 2013-06-22 PMC N PMC7161858 23483519.0 10.1002/bip.22230 ygzf1atu 0.946418 UNKNOWN_1987
2 Parthasarathy_2008 Transmembrane helices that form two opposite homodimeric interactions: An asparagine scan study of αM and β2 integrins Parthasarathy, Krupakar; Lin, Xin; Tan, Suet Mien; Law, S.K. Alex; Torres, Jaume 2008 2008-05-01 PMC N PMC2327277 18369198.0 10.1110/ps.073234208 rgfbee7h 0.859330 Ivarsson_2012, Smith_2003, UNKNOWN_1987, Yang_2012 Moulaei_2010
3 Parthasarathy_2008 Structural Flexibility of the Pentameric SARS Coronavirus Envelope Protein Ion Channel Parthasarathy, Krupakar; Ng, Lifang; Lin, Xin; Liu, Ding Xiang; Pervushin, Konstantin; Gong, Xiandi; Torres, Jaume 2008 2008-09-15 None N PMC2527252 18658207.0 10.1529/biophysj.108.133041 cqhytos1 0.854732 UNKNOWN_1987, UNKNOWN_1993, Ivarsson_2012, Gomis-Rüth_2003, UNKNOWN_1993 Torres_2007
4 Hsu_H_2014 Structure based computational assessment of channel properties of assembled ORF‐8a from SARS‐CoV Hsu, Hao‐Jen; Lin, Meng‐Han; Schindler, Christina; Fischer, Wolfgang B. 2014 2014-12-19 PMC N PMC7167713 25394339.0 10.1002/prot.24721 9wyoihk6 0.853120 UNKNOWN_1987, UNKNOWN_1993, Ivarsson_2012, Callison_1999, UNKNOWN_1993
5 Torres_2007 Conductance and amantadine binding of a pore formed by a lysine-flanked transmembrane domain of SARS coronavirus envelope protein Torres, Jaume; Maheswari, Uma; Parthasarathy, Krupakar; Ng, Lifang; Liu, Ding Xiang; Gong, Xiandi 2007 2007-09-01 PMC N PMC2206980 17766393.0 10.1110/ps.062730007 menw48x2 0.826103 UNKNOWN_1987, Chang_2000, UNKNOWN_1993, UNKNOWN_1993 Voß_D_2009, Guillén_2009
6 Torres_2006 Model of a Putative Pore: The Pentameric α-Helical Bundle of SARS Coronavirus E Protein in Lipid Bilayers Torres, Jaume; Parthasarathy, Krupakar; Lin, Xin; Saravanan, Rathi; Kukol, Andreas; Liu, Ding Xiang 2006 2006-08-01 None N PMC1563757 16698774.0 10.1529/biophysj.105.080119 nx0rx1v4 0.788347 UNKNOWN_1987, Ivarsson_2012, UNKNOWN_1993, Gomis-Rüth_2003 Torres_2007, Voß_D_2009
7 Gan_S_2008 Structure and ion channel activity of the human respiratory syncytial virus (hRSV) small hydrophobic protein transmembrane domain Gan, Siok Wan; Ng, Lifang; Lin, Xin; Gong, Xiandi; Torres, Jaume 2008 2008-05-01 PMC N PMC2327286 18369195.0 10.1110/ps.073366208 i5thcbze 0.694744 UNKNOWN_1987, Ivarsson_2012, Gomis-Rüth_2003, UNKNOWN_1993 Voß_D_2009
8 Chen_2011 ORF8a of SARS-CoV forms an ion channel: Experiments and molecular dynamics simulations Chen, Cheng-Chang; Krüger, Jens; Sramala, Issara; Hsu, Hao-Jen; Henklein, Peter; Chen, Yi-Ming Arthur; Fischer, Wolfgang B. 2011 2011-02-28 None N PMC7094593 20708597.0 10.1016/j.bbamem.2010.08.004 7aw17jf8 0.673506 Deng_2006, Ivarsson_2012, Wang_2014, UNKNOWN_1993 Chen_2009, Wang_2013
9 Gan_S_2014 Two Different Conformations in Hepatitis C Virus p7 Protein Account for Proton Transport and Dye Release Gan, Siok Wan; Surya, Wahyu; Vararattanavech, Ardcharaporn; Torres, Jaume 2014 2014-01-07 COMM-USE N PMC3883635 24409277.0 10.1371/journal.pone.0078494 e076c93q 0.662792 UNKNOWN_1987, Chang_2000, Gomis-Rüth_2003, UNKNOWN_1993 Wang_2013
10 Torres_2005 The Transmembrane Oligomers of Coronavirus Protein E Torres, Jaume; Wang, Jifeng; Parthasarathy, Krupakar; Liu, Ding Xiang 2005 2005-02-28 None N PMC1305130 15713601.0 10.1529/biophysj.104.051730 okm2fdyl 0.655751 UNKNOWN_1987, Ivarsson_2012, Yang_2012, Chang_2000 Voß_D_2009, Chen_2009
11 Lin_X_2006 Two types of transmembrane homomeric interactions in the integrin receptor family are evolutionarily conserved Lin, Xin; Tan, Suet Mien; Law, S.K. Alex; Torres, Jaume 2006 2006-01-27 PMC N PMC7168044 16444740.0 10.1002/prot.20882 np4nr7gg 0.651296 Ivarsson_2012, Parthasarathy_2008, Smith_2003
12 Verdiá-Báguena_2013 Analysis of SARS-CoV E protein ion channel activity by tuning the protein and lipid charge Verdiá-Báguena, Carmina; Nieto-Torres, Jose L.; Alcaraz, Antonio; DeDiego, Marta L.; Enjuanes, Luis; Aguilella, Vicente M. 2013 2013-09-30 PMC N PMC3715572 23688394.0 10.1016/j.bbamem.2013.05.008 ei61qlhy 0.648843 UNKNOWN_1987, UNKNOWN_1993, Ivarsson_2012, Yang_2012 Guillén_2009, Chen_2009, Voß_D_2009, Guillén_2008
13 Peng_2009 The strong dimerization of the transmembrane domain of the fibroblast growth factor receptor (FGFR) is modulated by C-terminal juxtamembrane residues Peng, Weng Chuan; Lin, Xin; Torres, Jaume 2009 2009-02-01 PMC N PMC2708062 19165726.0 10.1002/pro.65 pxk28u39 0.632633 Smith_2003, Ivarsson_2012, UNKNOWN_1987, Lawson_2012, Ospina_2011 Santiago_2007, Xiao_2004
14 Khattari_2006 SARS Coronavirus E Protein in Phospholipid Bilayers: An X-Ray Study Khattari, Z.; Brotons, G.; Akkawi, M.; Arbely, E.; Arkin, I.T.; Salditt, T. 2006 2006-03-15 None N PMC1386782 16361349.0 10.1529/biophysj.105.072892 u9wmzvkz 0.612637 Khattari_2006, Ivarsson_2012, UNKNOWN_1993 Voß_D_2009, Guillén_2009
15 Zunaid_2020 Significance of hydrophobic and charged sequence similarities in sodium-bile acid cotransporter and vitamin D-binding protein macrophage activating factor Ibne Raihan Zunaid; Stefania Pacini; Marco Ruggiero 2020 2020-03-05 BioRxiv N 10.1101/2020.03.03.975524 3ybko13r 0.603172 Ivarsson_2012, UNKNOWN_1987, Yang_2012, UNKNOWN_1993 Faaberg_1996
16 Hou_L_2014 Archaeal DnaG contains a conserved N-terminal RNA-binding domain and enables tailing of rRNA by the exosome Hou, Linlin; Klug, Gabriele; Evguenieva-Hackenberg, Elena 2014 2014-11-10 COMM-USE N PMC4227792 25326320.0 10.1093/nar/gku969 l1r416w7 0.595193
17 Pervushin_2009 Structure and Inhibition of the SARS Coronavirus Envelope Protein Ion Channel Pervushin, Konstantin; Tan, Edward; Parthasarathy, Krupakar; Lin, Xin; Jiang, Feng Li; Yu, Dejie; Vararattanavech, Ardcharaporn; Soong, Tuck Wah; Liu, Ding Xiang; Torres, Jaume 2009 2009-07-10 None N PMC2702000 19593379.0 10.1371/journal.ppat.1000511 1e102wrc 0.586697 UNKNOWN_1987, Chang_2000, Gomis-Rüth_2003 Voß_D_2009, Chen_2009
18 Surya_2015 MERS coronavirus envelope protein has a single transmembrane domain that forms pentameric ion channels Surya, Wahyu; Li, Yan; Verdià-Bàguena, Carmina; Aguilella, Vicente M.; Torres, Jaume 2015 2015-04-02 PMC N PMC7114494 25733052.0 10.1016/j.virusres.2015.02.023 bzk5im1z 0.582246 UNKNOWN_1987 Guillén_2009
19 Kim_Y_2018 Crystal structure of the natural anion-conducting channelrhodopsin GtACR1 Kim, Yoon Seok; Kato, Hideaki E.; Yamashita, Keitaro; Ito, Shota; inoue, Keiichi; Ramakrishnan, Charu; Fenno, Lief E.; Evans, Kathryn E.; Paggi, Joseph M.; Dror, Ron O.; Kandori, Hideki; Kobilka, Brian K.; Deisseroth, Karl 2018 2018-08-29 PMC N PMC6340299 30158696.0 10.1038/s41586-018-0511-6 lkts77ax 0.558701 Ivarsson_2012, Liu_Z_2008 Myllykoski_2017, Vicente_2015
20 Kosol_2010 Dynamics and orientation of a cationic antimicrobial peptide in two membrane-mimetic systems Kosol, Simone; Zangger, Klaus 2010 2010-04-30 PMC N PMC7128155 20045466.0 10.1016/j.jsb.2009.12.026 l8f4shar 0.549442 Ivarsson_2012, Ge_M_2011, Gomis-Rüth_2003, Wang_2014, UNKNOWN_1987 D’Errico_2009, Chang_2008
21 Hsu_H_2011 In silico investigations of possible routes of assembly of ORF 3a from SARS-CoV Hsu, Hao-Jen; Fischer, Wolfgang B. 2011 2011-05-04 PMC N PMC7087964 21541740.0 10.1007/s00894-011-1092-6 vdqq0j6l 0.542782 UNKNOWN_1987, Callison_1999, Ivarsson_2012, UNKNOWN_1993 Voß_D_2009, Guillén_2008, Chen_2009, RAMAKRISHNA_2015
22 Surya_2018 Structural model of the SARS coronavirus E channel in LMPG micelles Surya, Wahyu; Li, Yan; Torres, Jaume 2018 2018-06-30 None N PMC7094280 29474890.0 10.1016/j.bbamem.2018.02.017 rnaktik9 0.538499 UNKNOWN_1987, Callison_1999, Gomis-Rüth_2003, Yang_2012 Guillén_2009, Voß_D_2009, Surya_2015
23 Kalita_2015 Genotype-specific differences in structural features of hepatitis C virus (HCV) p7 membrane protein Kalita, Monoj Mon; Griffin, Stephen; Chou, James J.; Fischer, Wolfgang B. 2015 2015-06-30 PMC N PMC7094707 25772504.0 10.1016/j.bbamem.2015.03.006 09csacgb 0.529637 Callison_1999, UNKNOWN_1987, Gomis-Rüth_2003, UNKNOWN_1993 Wang_2013
24 Lee_C_2014 Crowning Proteins: Modulating the Protein Surface Properties using Crown Ethers** Lee, Cheng-Chung; Maestre-Reyna, Manuel; Hsu, Kai-Cheng; Wang, Hao-Ching; Liu, Chia-I; Jeng, Wen-Yih; Lin, Li-Ling; Wood, Richard; Chou, Chia-Cheng; Yang, Jinn-Moon; Wang, Andrew H-J 2014 2014-11-24 NONCOMM N PMC4288931 25287606.0 10.1002/anie.201405664 anivjq7i 0.504263 Langosch_2011, Ivarsson_2012, Deng_2008 Moulaei_2010, Robinson_2013
25 Le_T_2007 Expression, post‐translational modification and biochemical characterization of proteins encoded by subgenomic mRNA8 of the severe acute respiratory syndrome coronavirus Le, Tra M.; Wong, Hui H.; Tay, Felicia P. L.; Fang, Shouguo; Keng, Choong‐Tat; Tan, Yee J.; Liu, Ding X. 2007 2007-07-20 PMC N PMC7164070 17645546.0 10.1111/j.1742-4658.2007.05947.x 5fh477c4 0.478576 UNKNOWN_1987
26 RAMAKRISHNA_2015 Modeling the structure of SARS 3a transmembrane protein using a minimum unfavorable contact approach RAMAKRISHNA, S; PADHI, SILADITYA; PRIYAKUMAR, U DEVA 2015 2015-12-09 PMC N PMC7090505 10.1007/s12039-015-0982-z gbnns8np 0.472324 Ivarsson_2012, UNKNOWN_1987, Callison_1999 Wang_2013, Voß_D_2009, Guillén_2009
27 Liu_D_2017 Topology Engineering of Proteins in Vivo Using Genetically Encoded, Mechanically Interlocking SpyX Modules for Enhanced Stability Liu, Dong; Wu, Wen-Hao; Liu, Ya-Jie; Wu, Xia-Ling; Cao, Yang; Song, Bo; Li, Xiaopeng; Zhang, Wen-Bin 2017 2017-05-10 None N PMC5445526 28573210.0 10.1021/acscentsci.7b00104 xonthuw5 0.464404 Ivarsson_2012, UNKNOWN_1987, Wang_2014, Smith_2003, Gomis-Rüth_2003 Kuo_D_2011, Strong_1991
28 Khattari_2006 Viral ion channel proteins in model membranes: a comparative study by X-ray reflectivity Khattari, Z.; Arbely, E.; Arkin, I. T.; Salditt, T. 2006 2006-09-21 PMC N PMC7080166 17019591.0 10.1007/s00249-006-0099-x yqnbybh0 0.457600 Ge_M_2011, Ivarsson_2012 Chang_2008, Khattari_2006
29 Popot_1993 Integral membrane protein structure: transmembrane α-helices as autonomous folding domains Current opinion in structural biology 1993, 3: 532–540 Popot, Jean-Luc 1993 1993-08-31 PMC N PMC7126879 10.1016/0959-440x(93)90079-z cx0m54dd 0.453201 Ivarsson_2012, UNKNOWN_1987, UNKNOWN_1993, Modis_2013 Faaberg_1996, UNKNOWN_1995
30 Cai_C_2006 Prediction of Transmembrane Proteins from Their Primary Sequence by Support Vector Machine Approach Cai, C. Z.; Yuan, Q. F.; Xiao, H. G.; Liu, X. H.; Han, L. Y.; Chen, Y. Z. 2006 2006-01-01 PMC N PMC7121931 10.1007/11816102_56 rktwtqtq 0.426442 Lee_B_2009, Wang_2013
31 Zeng_2004 Characterization of the 3a Protein of SARS-associated Coronavirus in Infected Vero E6 Cells and SARS Patients Zeng, Rong; Yang, Rui-Fu; Shi, Mu-De; Jiang, Man-Rong; Xie, You-Hua; Ruan, Hong-Qiang; Jiang, Xiao-Sheng; Shi, Lv; Zhou, Hu; Zhang, Lei; Wu, Xiao-Dong; Lin, Ying; Ji, Yong-Yong; Xiong, Lei; Jin, Yan; Dai, Er-Hei; Wang, Xiao-Yi; Si, Bin-Ying; Wang, Jin; Wang, Hong-Xia; Wang, Cui-E; Gan, Yong-Hua; Li, Yu-Chuan; Cao, Ju-Tian; Zuo, Jiang-Ping; Shan, Shi-Fang; Xie, En; Chen, Song-Hua; Jiang, Zhi-Qin; Zhang, Xi; Wang, Yuan; Pei, Gang; Sun, Bing; Wu, Jia-Rui 2004 2004-07-30 PMC N PMC7127270 15312778.0 10.1016/j.jmb.2004.06.016 me5ff1pb 0.425514 Liu_M_2006
32 Abad_2009 Membrane topology of gp41 and amyloid precursor protein: Interfering transmembrane interactions as potential targets for HIV and Alzheimer treatment Abad, Concepción; Martínez-Gil, Luis; Tamborero, Silvia; Mingarro, Ismael 2009 2009-10-31 PMC N PMC7094694 19619504.0 10.1016/j.bbamem.2009.07.008 z4zt5873 0.420124 Ivarsson_2012, UNKNOWN_1987, Chang_2000, UNKNOWN_1993 Voß_D_2009, Chen_2009, Guillén_2009
33 MacKenzie_2008 Association energetics of membrane spanning α-helices MacKenzie, Kevin R; Fleming, Karen G 2008 2008-08-31 PMC N PMC7127525 18539023.0 10.1016/j.sbi.2008.04.007 61cs7r9f 0.416399 Langosch_2011, Deng_2008, Ivarsson_2012 Langosch_2011, Chang_2008
34 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 0.411219 Fernando_2008 Myllykoski_2017
35 Sugrue_1991 Structural characteristics of the M2 protein of influenza a viruses: Evidence that it forms a tetrameric channe Sugrue, R.J.; Hay, A.J. 1991 1991-02-28 PMC N PMC7131614 1989386.0 10.1016/0042-6822(91)90075-m y7t47t7a 0.401773 Ivarsson_2012, Gomis-Rüth_2003, UNKNOWN_1987 Voß_D_2009
36 Khattari_2005 SARS E protein in phospholipid bilayers: an anomalous X-ray reflectivity study Khattari, Z.; Brotons, G.; Arbely, E.; Arkin, I.T.; Metzger, T.H.; Salditt, T. 2005 2005-02-28 PMC N PMC7127356 10.1016/j.physb.2004.11.015 hi8k8wvb 0.394412 Khattari_2006, UNKNOWN_1993, Ge_M_2011 Khattari_2006, Khattari_2006, Schneggenburger_2010, D’Errico_2009
37 Wang_2013 Computational modeling of the p7 monomer from HCV and its interaction with small molecule drugs Wang, Yi-Ting; Hsu, Hao-Jen; Fischer, Wolfgang B 2013 2013-07-18 COMM-USE N PMC3724979 23961398.0 10.1186/2193-1801-2-324 zwdmd7uf 0.368591 UNKNOWN_1987, Ivarsson_2012, Smith_2003, Chang_2000 Guillén_2009, D’Errico_2009
38 Yuan_2006 Biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells Yuan, Q.; Liao, Y.; Torres, J.; Tam, J.P.; Liu, D.X. 2006 2006-05-29 PMC N PMC7094218 16684538.0 10.1016/j.febslet.2006.04.076 v3lbrzh8 0.368591 UNKNOWN_1987, Maeda_2001, UNKNOWN_1993, UNKNOWN_1993 Voß_D_2009, Chen_2009
39 Ghosh_2018 Structural insights of a self-assembling 9-residue peptide from the C-terminal tail of the SARS corona virus E-protein in DPC and SDS micelles: A combined high and low resolution spectroscopic study Ghosh, Anirban; Bhattacharyya, Dipita; Bhunia, Anirban 2018 2018-02-28 None N PMC7094419 29038024.0 10.1016/j.bbamem.2017.10.015 kk1pk8fn 0.365597 Gomis-Rüth_2003, UNKNOWN_1987, Ivarsson_2012 Voß_D_2009, Guillén_2009, Vazquez_2017
40 Rettinger_2016 Examples of Applications of Electrophysiology Rettinger, Jürgen; Schwarz, Silvia; Schwarz, Wolfgang 2016 2016-06-03 PMC N PMC7123767 10.1007/978-3-319-30012-2_8 subm50ld 0.345765 Ivarsson_2012, Liu_Z_2008
41 Parthasarathy_2012 Expression and purification of coronavirus envelope proteins using a modified β-barrel construct Parthasarathy, Krupakar; Lu, Huang; Surya, Wahyu; Vararattanavech, Ardcharaporn; Pervushin, Konstantin; Torres, Jaume 2012 2012-09-30 PMC N PMC7129850 22819936.0 10.1016/j.pep.2012.07.005 4jg4t8po 0.341437 UNKNOWN_1987, Chang_2000, Yang_2012 Chen_2009, Voß_D_2009
42 Martinez-Gil_2015 Viroporins, Examples of the Two-Stage Membrane Protein Folding Model Martinez-Gil, Luis; Mingarro, Ismael 2015 2015-06-26 COMM-USE N PMC4517110 26131957.0 10.3390/v7072781 vcb6d6bv 0.326809 Modis_2013, Ivarsson_2012 Voß_D_2009
43 Ruch_2012 A Single Polar Residue and Distinct Membrane Topologies Impact the Function of the Infectious Bronchitis Coronavirus E Protein Ruch, Travis R.; Machamer, Carolyn E. 2012 2012-05-03 COMM-USE N PMC3343006 22570613.0 10.1371/journal.ppat.1002674 tro7b4d0 0.315402 UNKNOWN_1987, Gomis-Rüth_2003 Voß_D_2009
44 Liu_H_2008 A new approach to the prediction of transmembrane structures Liu, HongDe; Wang, Rui; Lu, XiaoQuan; Chen, Jing; Liu, Xiuhui; Ding, Lan 2008 2008-05-23 PMC N PMC7088861 10.1007/s11434-008-0055-5 n10ia3j3 0.300624 UNKNOWN_1987 Wang_2013, Cai_C_2006, RAMAKRISHNA_2015