Topic 05 -- 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 Chen_2010 Discovery of anti‐SARS coronavirus drug based on molecular docking and database screening Chen, Hai‐Feng; Yao, Jian‐Hua; Sun, Jing; Li, Qiang; Li, Feng; Fan, Bo‐Tao; Yuan, Shen‐Gang 2010 2010-08-26 PMC N PMC7162226 10.1002/cjoc.20040220825 go2tsomq 0.910930 Callison_1999
2 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 0.856625 Smith_2003, Gomis-Rüth_2003, Ivarsson_2012, UNKNOWN_1987 Kanitz_2019
3 Aliebrahimi_2017 Identification of Phytochemicals Targeting c-Met Kinase Domain using Consensus Docking and Molecular Dynamics Simulation Studies Aliebrahimi, Shima; Montasser Kouhsari, Shideh; Ostad, Seyed Nasser; Arab, Seyed Shahriar; Karami, Leila 2017 2017-08-29 PMC N PMC7090793 28852971.0 10.1007/s12013-017-0821-6 lfmtmqju 0.854131 Smith_2003, Ivarsson_2012, Choudhury_2017
4 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 0.840456 Ivarsson_2012, Chan_2016, UNKNOWN_1987, Callison_1999
5 Macchiagodena_2020 Identification of Potential Binders of the Main Protease 3CLpro of the COVID-19 via Structure-Based Ligand Design and Molecular Modeling Macchiagodena, Marina; Pagliai, Marco; Procacci, Piero 2020 2020-04-18 PMC Y 10.1016/j.cplett.2020.137489 3t577va2 0.825276 Ivarsson_2012, Kinjo_2012
6 Ye_Y_2007 Computational studies of the binding modes of A(2A) adenosine receptor antagonists Ye, Y.; Wei, J.; Dai, X.; Gao, Q. 2007 2007-11-05 PMC N PMC7087644 17978889.0 10.1007/s00726-007-0604-2 7261eu96 0.802601 Ivarsson_2012, Kinjo_2012 Li_G_2009
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 0.767615 Smith_2003, Ivarsson_2012, UNKNOWN_1987, Wang_2014
8 Berry_2015 Human coronavirus OC43 3CL protease and the potential of ML188 as a broad-spectrum lead compound: Homology modelling and molecular dynamic studies Berry, Michael; Fielding, Burtram; Gamieldien, Junaid 2015 2015-04-28 COMM-USE N PMC4411765 25928480.0 10.1186/s12900-015-0035-3 26jg9g0b 0.766903 Callison_1999
9 Odhar_2020 Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus Odhar, Hasanain Abdulhameed; Ahjel, Salam Waheed; Albeer, Ali A.Mohammed Ali; Hashim, Ahmed Fadhil; Rayshan, Ali Mahmood; Humadi, Suhad Sami 2020 2020-03-31 COMM-USE Y PMC7147498 10.6026/97320630016236 8xi5k7f2 0.766766 Ivarsson_2012, Liu_Z_2008
10 Liou_2014 In Silico Analysis Reveals Sequential Interactions and Protein Conformational Changes during the Binding of Chemokine CXCL-8 to Its Receptor CXCR1 Liou, Je-Wen; Chang, Fang-Tzu; Chung, Yi; Chen, Wen-Yi; Fischer, Wolfgang B.; Hsu, Hao-Jen 2014 2014-04-04 COMM-USE N PMC3976404 24705928.0 10.1371/journal.pone.0094178 yuv8h375 0.765863 Ivarsson_2012, Smith_2003, Snyder_2005, UNKNOWN_1987 Wang_2013, Moulaei_2010, Li_G_2009
11 Yang_2010 Long range interaction networks in the function and fidelity of poliovirus RNA-dependent RNA polymerase studied by nuclear magnetic resonance Yang, Xiaorong; Welch, Jesse L.; Arnold, Jamie J.; Boehr, David D. 2010 2010-11-02 PMC N PMC2989882 20860410.0 10.1021/bi100833r 7fpantqv 0.745407 Chan_2016
12 Ye_F_2018 Molecular basis of binding between the global post-transcriptional regulator CsrA and the T3SS chaperone CesT Ye, Fei; Yang, Fanli; Yu, Ruijie; Lin, Xi; Qi, Jianxun; Chen, Zhujun; Cao, Yu; Wei, Yuquan; Gao, George F.; Lu, Guangwen 2018 2018-03-22 COMM-USE N PMC5864733 29567971.0 10.1038/s41467-018-03625-x 6gem43t0 0.742765 Ivarsson_2012, Smith_2003, Choudhury_2017
13 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 0.742223 Smith_2003, Yang_2012, Callison_1999, UNKNOWN_1987, Ivarsson_2012
14 Jankauskaitė_2018 SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation Justina Jankauskaitė; Brian Jiménez-García; Justas Dapkūnas; Juan Fernández-Recio; Iain H. Moal 2018 2018-06-07 BioRxiv N 10.1101/341735 d0eynz67 0.737682 Ivarsson_2012, Smith_2003, Chan_2016, Kinjo_2012 Jankauskaitė_2019, Myllykoski_2017
15 Siqueira_2017 In silico analysis of the cyanobacterial lectin scytovirin: new insights into binding properties Siqueira, Andrei Santos; Lima, Alex Ranieri Jerônimo; de Souza, Rafael Conceição; Santos, Alberdan Silva; Vianez Júnior, João Lídio da Silva Gonçalves; Gonçalves, Evonnildo Costa 2017 2017-07-29 PMC N PMC7088960 28756560.0 10.1007/s11033-017-4116-1 iz9klwvp 0.723277 Callison_1999, UNKNOWN_1987 Yap_Y_2005
16 Wang_2007 Accurate Reproduction of 161 Small-Molecule Complex Crystal Structures using the EUDOC Program: Expanding the Use of EUDOC to Supramolecular Chemistry Wang, Qi; Pang, Yuan-Ping 2007 2007-06-13 COMM-USE N PMC1888730 17565384.0 10.1371/journal.pone.0000531 be2ith3z 0.704876 Ivarsson_2012, Kinjo_2012, Chan_2016 Wang_2013, Li_G_2009
17 Chaudhuri_2011 Comparison of SARS and NL63 Papain-Like Protease Binding Sites and Binding Site Dynamics: Inhibitor Design Implications Chaudhuri, Rima; Tang, Sishi; Zhao, Guijun; Lu, Hui; Case, David A.; Johnson, Michael E. 2011 2011-11-25 None N PMC3397151 22004941.0 10.1016/j.jmb.2011.09.030 snldtqsn 0.703336 Smith_2003, Ivarsson_2012, Chan_2016, Wang_2014
18 Wang_2010 On the mechanisms of bananin activity against severe acute respiratory syndrome coronavirus Wang, Zai; Huang, Jian‐Dong; Wong, Kin‐Ling; Wang, Pei‐Gang; Zhang, Hao‐Jie; Tanner, Julian A.; Spiga, Ottavia; Bernini, Andrea; Zheng, Bo‐Jian; Niccolai, Neri 2010 2010-12-06 PMC N PMC7164005 21134131.0 10.1111/j.1742-4658.2010.07961.x aaht8rq0 0.696524 Smith_2003, UNKNOWN_1987
19 Vy_T_2020 Spontaneous Hinge-Bending Motions of Angiotensin I Converting Enzyme: Role in Activation and Inhibition Vy, Thi Tuong; Heo, Seong-Yeong; Jung, Won-Kyo; Yi, Myunggi 2020 2020-03-12 COMM-USE N PMC7146279 32178362.0 10.3390/molecules25061288 fm01bijc 0.696122 Ivarsson_2012, Chan_2016, Smith_2003
20 Kingsley_2016 Ranking Protein-Protein Docking Results using Steered Molecular Dynamics and Potential of Mean Force Calculations Kingsley, Laura J.; Esquivel-Rodríguez, Juan; Yang, Ying; Kihara, Daisuke; Lill, Markus A. 2016 2016-05-27 PMC N PMC5015890 27232548.0 10.1002/jcc.24412 04t18oqp 0.692608 Wang_2013, RAMAKRISHNA_2015, Zhang_2018
21 Gupta_2015 NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics Gupta, Garvita; Lim, Liangzhong; Song, Jianxing 2015 2015-08-10 COMM-USE N PMC4530887 26258523.0 10.1371/journal.pone.0134823 bbeznd3r 0.670310 Gomis-Rüth_2003, Ivarsson_2012
22 Chou_2014 Structural basis for catalysis and ubiquitin recognition by the Severe acute respiratory syndrome coronavirus papain‐like protease Chou, Chi‐Yuan; Lai, Hsing‐Yi; Chen, Hung‐Yi; Cheng, Shu‐Chun; Cheng, Kai‐Wen; Chou, Ya‐Wen 2014 2014-02-17 PMC N PMC7161584 24531491.0 10.1107/s1399004713031040 o60cr7jj 0.665650 Smith_2003, Ivarsson_2012, UNKNOWN_1987
23 Glantz-Gashai_2017 Virtual screening for potential inhibitors of Mcl-1 conformations sampled by normal modes, molecular dynamics, and nuclear magnetic resonance Glantz-Gashai, Yitav; Meirson, Tomer; Reuveni, Eli; Samson, Abraham O 2017 2017-06-19 NONCOMM N PMC5484510 28684899.0 10.2147/dddt.s133127 47srfqzl 0.647083 Liu_Z_2008, Ivarsson_2012
24 Elfiky_2019 Novel guanosine derivatives against Zika virus polymerase in silico Elfiky, Abdo A. 2019 2019-08-29 PMC N PMC7166851 31436327.0 10.1002/jmv.25573 qpq7i1ya 0.641167
25 Li_G_2009 A Comparative Docking Study of Anibamine as the First Natural Product CCR5 Antagonist in CCR5 Homology Models Li, Guo; Haney, Kendra M.; Kellogg, Glen E.; Zhang, Yan 2009 2009-01-26 PMC N PMC2656111 19166361.0 10.1021/ci800356a 75o3z87q 0.640728 Ivarsson_2012
26 Wang_2011 Insights from Modeling the 3D Structure of New Delhi Metallo-β-Lactamse and Its Binding Interactions with Antibiotic Drugs Wang, Jing-Fang; Chou, Kuo-Chen 2011 2011-04-11 COMM-USE N PMC3073942 21494599.0 10.1371/journal.pone.0018414 qifqc89z 0.633999 Ivarsson_2012, Callison_1999, Kirillova_2009 Wang_2013
27 Tan_J_2005 pH-dependent Conformational Flexibility of the SARS-CoV Main Proteinase (Mpro) Dimer: Molecular Dynamics Simulations and Multiple X-ray Structure Analyses Tan, Jinzhi; Verschueren, Koen H.G.; Anand, Kanchan; Shen, Jianhua; Yang, Maojun; Xu, Yechun; Rao, Zihe; Bigalke, Janna; Heisen, Burkhard; Mesters, Jeroen R.; Chen, Kaixian; Shen, Xu; Jiang, Hualiang; Hilgenfeld, Rolf 2005 2005-11-18 PMC N PMC7094468 16242152.0 10.1016/j.jmb.2005.09.012 uvuamh0p 0.625272 Chan_2016, Ivarsson_2012, Smith_2003 Lin_P_2008
28 Jankauskaitė_2019 SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation Jankauskaitė, Justina; Jiménez-García, Brian; Dapkūnas, Justas; Fernández-Recio, Juan; Moal, Iain H 2019 2019-02-01 COMM-USE N PMC6361233 30020414.0 10.1093/bioinformatics/bty635 vqiipbo8 0.622287 Ivarsson_2012, Callison_1999 Jankauskaitė_2018, Myllykoski_2017
29 Tambunan_2014 In silico modification of oseltamivir as neuraminidase inhibitor of influenza A virus subtype H1N1 Tambunan, Usman Sumo Friend; Rachmania, Rizky Archintya; Parikesit, Arli Aditya 2014 2014-12-12 PMC N PMC4389116 25859271.0 10.7555/jbr.29.20130024 3gz4dyie 0.610431
30 Myllykoski_2017 Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase Myllykoski, Matti; Kursula, Petri 2017 2017-01-31 COMM-USE N PMC5283653 28141848.0 10.1371/journal.pone.0170355 0a3okta0 0.600649 Ivarsson_2012, Smith_2003, Chan_2016, Sundaramoorthy_2018 Kanitz_2019
31 Guo_H_2007 Computational studies for the structure and function of mRPE65 Guo, Hao; Zheng, Chong; Gaillard, Elizabeth R. 2007 2007-03-21 PMC N PMC7094118 17123547.0 10.1016/j.jtbi.2006.10.002 mfm96d2q 0.580747 Ivarsson_2012, Kirillova_2009, Liu_Z_2008 Myllykoski_2017, RAMAKRISHNA_2015
32 Wang_2018 A Comprehensive In Silico Method to Study the QSTR of the Aconitine Alkaloids for Designing Novel Drugs Wang, Ming-Yang; Liang, Jing-Wei; Mohamed Olounfeh, Kamara; Sun, Qi; Zhao, Nan; Meng, Fan-Hao 2018 2018-09-18 COMM-USE N PMC6225272 30231506.0 10.3390/molecules23092385 fewy8y4a 0.575526 Liu_Z_2008
33 Zhang_2018 Exploring the Binding Mechanism between Human Profilin (PFN1) and Polyproline-10 through Binding Mode Screening Leili Zhang; David R. Bell; Binquan Luan; Ruhong Zhou 2018 2018-09-16 BioRxiv N 10.1101/418830 40pe21lm 0.571783 Wang_2013, Yap_Y_2005
34 Jin_F_2013 Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins Jin, Fan; Yu, Chen; Lai, Luhua; Liu, Zhirong 2013 2013-10-03 COMM-USE N PMC3789766 24098099.0 10.1371/journal.pcbi.1003249 5l0fthw3 0.558413 Ivarsson_2012, Smith_2003, Chan_2016, Kirillova_2009 Wang_2013, RAMAKRISHNA_2015, Liou_2014
35 Li_X_2011 Novel Inhibitor Design for Hemagglutinin against H1N1 Influenza Virus by Core Hopping Method Li, Xiao-Bo; Wang, Shu-Qing; Xu, Wei-Ren; Wang, Run-Ling; Chou, Kuo-Chen 2011 2011-11-30 COMM-USE N PMC3227604 22140516.0 10.1371/journal.pone.0028111 16syz1o7 0.535332
36 Roy_A_2016 Unique properties of Zika NS2B-NS3pro complexes as decoded by experiments and MD simulations Amrita Roy; Liangzhong Lim; Shagun Srivastava; Jianxing Song 2016 2016-09-28 BioRxiv N 10.1101/078113 l82aakrk 0.534700 Gomis-Rüth_2003
37 Roy_K_2015 Chapter 10 Other Related Techniques Roy, Kunal; Kar, Supratik; Das, Rudra Narayan 2015 2015-12-31 PMC N PMC7149793 10.1016/b978-0-12-801505-6.00010-7 a9q0tcgz 0.532898 Liu_Z_2008 Zhang_2018
38 Hoffmann_2006 Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors Hoffmann, Marcin; Eitner, Krystian; von Grotthuss, Marcin; Rychlewski, Leszek; Banachowicz, Ewa; Grabarkiewicz, Tomasz; Szkoda, Tomasz; Kolinski, Andrzej 2006 2006-09-14 PMC N PMC7088412 16972168.0 10.1007/s10822-006-9057-z ij5xrtzx 0.528723 Ivarsson_2012, Kinjo_2012, Smith_2003, Chan_2016 Kanitz_2019
39 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 0.511309 Smith_2003, Ivarsson_2012, Yang_2012, UNKNOWN_1987, Chan_2016 Kanitz_2019
40 Guo_L_2015 Interaction Behavior Between Niclosamide and Pepsin Determined by Spectroscopic and Docking Methods Guo, Liuqi; Ma, Xiaoli; Yan, Jin; Xu, Kailin; Wang, Qing; Li, Hui 2015 2015-09-26 PMC N PMC7087788 26410777.0 10.1007/s10895-015-1655-5 83t5mlpr 0.511147 Chan_2016, Ivarsson_2012, Smith_2003, Langosch_2011 Maltas_2014, Moulaei_2010, Vicente_2015
41 Wells_2020 Rigidity, normal modes and flexible motion of a SARS-CoV-2 (COVID-19) protease structure Stephen A. Wells 2020 2020-03-12 BioRxiv Y 10.1101/2020.03.10.986190 rzda8x62 0.494371 Liu_Z_2008 Phakthanakanok_2009
42 Park_2013 Accurate Structure Prediction of Peptide-MHC Complexes for Identifying Highly Immunogenic Antigens Park, Min-Sun; Park, Sung Yong; Miller, Keith R.; Collins, Edward J.; Lee, Ha Youn 2013 2013-11-01 PMC N PMC3686981 23688437.0 10.1016/j.molimm.2013.04.011 1v2wcxck 0.482892 Ivarsson_2012 Yu_M_2000
43 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 0.480811 Ivarsson_2012, Smith_2003, Chan_2016, Choudhury_2017, UNKNOWN_1987 Kanitz_2019
44 Lin_S_2020 Structure-Based Stabilization of Non-native Protein–Protein Interactions of Coronavirus Nucleocapsid Proteins in Antiviral Drug Design Lin, Shan-Meng; Lin, Shih-Chao; Hsu, Jia-Ning; Chang, Chung-ke; Chien, Ching-Ming; Wang, Yong-Sheng; Wu, Hung-Yi; Jeng, U-Ser; Kehn-Hall, Kylene; Hou, Ming-Hon 2020 2020-02-27 PMC N PMC7094172 32105468.0 10.1021/acs.jmedchem.9b01913 rn4gm3sc 0.480269 Ivarsson_2012, Smith_2003, Langosch_2011, Gomis-Rüth_2003 Wang_2013, Voß_D_2009
45 Wang_2010 Molecular simulation study of the binding mechanism of [α-PTi(2)W(10)O(40)](7−) for its promising broad-spectrum inhibitory activity to FluV-A neuraminidase Wang, JianPing; Hu, DongHua; Su, ZhongMin 2010 2010-08-14 PMC N PMC7089260 10.1007/s11434-010-3271-8 5wieasp8 0.474582 Callison_1999, Ivarsson_2012, Smith_2003, Chan_2016, UNKNOWN_1987
46 Liu_H_2013 Homology Models and Molecular Dynamics Simulations of Main Proteinase from Coronavirus Associated with Severe Acute Respiratory Syndrome (SARS) Liu, Hsuan‐Liang; Lin, Jin‐Chung; Ho, Yih; Hsieh, Wei‐Chan; Chen, Chin‐Wen; Su, Yuan‐Chen 2013 2013-09-25 PMC Y PMC7167048 10.1002/jccs.200400134 zjvk1p1s 0.467362 Callison_1999, Ivarsson_2012, UNKNOWN_1987
47 Vajda_2018 Cryptic binding sites on proteins: definition, detection, and druggability Vajda, Sandor; Beglov, Dmitri; Wakefield, Amanda E; Egbert, Megan; Whitty, Adrian 2018 2018-06-30 PMC N PMC6088748 29800865.0 10.1016/j.cbpa.2018.05.003 1csbxa8f 0.456260 Liu_Z_2008, Kirillova_2009
48 Bassetto_2016 Structural biology in antiviral drug discovery Bassetto, Marcella; Massarotti, Alberto; Coluccia, Antonio; Brancale, Andrea 2016 2016-10-31 PMC N 27611878.0 10.1016/j.coph.2016.08.014 3eoio8uk 0.435448 Ivarsson_2012, Liu_Z_2008 Robinson_2013
49 Ho_S_2009 Structural bioinformatics analysis of free cysteines in protein environments Ho, Sheau Ling; Wang, Andrew H.-J. 2009 2009-03-31 PMC N PMC7102755 10.1016/j.jtice.2008.07.015 2hx4fuk2 0.433638 Yang_2012, Ivarsson_2012, UNKNOWN_1987, Smith_2003
50 Yap_Y_2005 Structural analysis of inhibition mechanisms of Aurintricarboxylic Acid on SARS-CoV polymerase and other proteins Yap, YeeLeng; Zhang, XueWu; Andonov, Anton; He, RunTao 2005 2005-06-30 PMC N PMC7106521 15979041.0 10.1016/j.compbiolchem.2005.04.006 8c05w1ix 0.433106
51 Hognon_2020 Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses Cécilia Hognon; Tom Miclot; Cristina Garcia Iriepa; Antonio Francés-Monerris; Stephanie Grandemange; Alessio Terenzi; Marco Marazzi; Giampaolo Barone; Antonio Monari 2020 2020-04-10 BioRxiv Y 10.1101/2020.04.07.029447 dnppshnv 0.433049 Chan_2016, Ivarsson_2012 Guillén_2009
52 Bzówka_2020 Molecular Dynamics Simulations Indicate the SARS-CoV-2 Mpro Is Not a Viable Target for Small-Molecule Inhibitors Design Maria Bzówka; Karolina Mitusińska; Agata Raczyńska; Aleksandra Samol; Jack Tuszyński; Artur Góra 2020 2020-03-02 BioRxiv Y 10.1101/2020.02.27.968008 mp3a9c9u 0.410825 Kirillova_2009, Liu_Z_2008
53 Kanitz_2019 Structural basis for catalysis and substrate specificity of a 3C-like cysteine protease from a mosquito mesonivirus Kanitz, Manuel; Blanck, Sandra; Heine, Andreas; Gulyaeva, Anastasia A.; Gorbalenya, Alexander E.; Ziebuhr, John; Diederich, Wibke E. 2019 2019-07-31 None N PMC7111312 31078932.0 10.1016/j.virol.2019.05.001 1ksfo0pr 0.407912 Smith_2003, Ivarsson_2012, UNKNOWN_1987
54 Kim_M_2013 A mass weighted chemical elastic network model elucidates closed form domain motions in proteins Kim, Min Hyeok; Seo, Sangjae; Jeong, Jay Il; Kim, Bum Joon; Liu, Wing Kam; Lim, Byeong Soo; Choi, Jae Boong; Kim, Moon Ki 2013 2013-03-18 PMC N PMC3649262 23456820.0 10.1002/pro.2244 p8n8va3y 0.407912 Kirillova_2009 Mascarenhas_2017, RAMAKRISHNA_2015, CAO_S_2012, Eddy_2018
55 Feng_2013 A Study of the Mechanism of the Chaperone-like Function of an scFv of Human Creatine Kinase by Computer Simulation Feng, Jianyu; Guo, Hong; Li, Sen; Lu, Tun 2013 2013-04-24 COMM-USE N PMC3634753 23637984.0 10.1371/journal.pone.0062147 psguw47w 0.401831 Ivarsson_2012, Smith_2003, Choudhury_2017, UNKNOWN_1987
56 Kuhn_2006 From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase Kuhn, Daniel; Weskamp, Nils; Schmitt, Stefan; Hüllermeier, Eyke; Klebe, Gerhard 2006 2006-06-16 PMC N PMC7094329 16697007.0 10.1016/j.jmb.2006.04.024 h7leow0q 0.401253 Ivarsson_2012, Liu_Z_2008, Kinjo_2012 Myllykoski_2017, Ziółkowska_2006
57 Kandeel_2018 Molecular dynamics of Middle East Respiratory Syndrome Coronavirus (MERS CoV) fusion heptad repeat trimers Kandeel, Mahmoud; Al-Taher, Abdulla; Li, Huifang; Schwingenschlogl, Udo; Al-Nazawi, Mohamed 2018 2018-08-31 PMC N PMC7106505 29803965.0 10.1016/j.compbiolchem.2018.05.020 e2wkol48 0.399865 Zhang_2018, Deng_2006, Callison_1999, UNKNOWN_1987 Channappanavar_2015, Lu_L_2014
58 Ziółkowska_2007 Crystallographic studies of the complexes of antiviral protein griffithsin with glucose and N-acetylglucosamine Ziółkowska, Natasza E.; Shenoy, Shilpa R.; O'Keefe, Barry R.; Wlodawer, Alexander 2007 2007-07-01 PMC N PMC2206701 17567736.0 10.1110/ps.072889407 8qd1a997 0.396979 Ivarsson_2012, Chan_2016, Tosoni_2015, UNKNOWN_1987 Moulaei_2010, Ziółkowska_2006
59 Zaucha_2020 Deep learning model can predict water binding sites on the surface of proteins using limited-resolution data Jan Zaucha; Charlotte A. Softley; Michael Sattler; Grzegorz M. Popowicz 2020 2020-04-21 BioRxiv Y 10.1101/2020.04.20.050393 sy3n8v7f 0.391205 Kirillova_2009
60 Shokhen_2009 Challenging a Paradigm: Theoretical Calculations of the Protonation State of the Cys25-His159 Catalytic Diad in Free Papain Shokhen, Michael; Khazanov, Netaly; Albeck, Amnon 2009 2009-12-01 PMC N PMC2767454 19688822.0 10.1002/prot.22516 h8qsila6 0.389822 Smith_2003, Ho_S_2009, Ivarsson_2012 Kanitz_2019, Myllykoski_2017
61 Lupala_2020 Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein Cecylia S. Lupala; Xuanxuan Li; Jian Lei; Hong Chen; Jianxun Qi; Haiguang Liu; Xiao-dong Su 2020 2020-03-27 BioRxiv Y 10.1101/2020.03.24.005561 kifqgskc 0.389576 Ivarsson_2012, UNKNOWN_1987, Callison_1999, Smith_2003 Zhang_2009, Guillén_2009, Chowdhury_2020, Wang_2020
62 Chitrala_2019 Computational prediction and in vitro validation of VEGFR1 as a novel protein target for 2,3,7,8-tetrachlorodibenzo-p-dioxin Chitrala, Kumaraswamy Naidu; Yang, Xiaoming; Busbee, Brandon; Singh, Narendra P.; Bonati, Laura; Xing, Yongna; Nagarkatti, Prakash; Nagarkatti, Mitzi 2019 2019-05-02 COMM-USE N PMC6497656 31048752.0 10.1038/s41598-019-43232-4 sib13c9c 0.385977 Ivarsson_2012, Choudhury_2017
63 Lung_2020 The potential SARS-CoV-2 entry inhibitor Jrhau Lung; Yu-Shih Lin; Yao-Hsu Yang; Yu-Lun Chou; Geng-He Chang; Ming-Shao Tsai; Cheng-Ming Hsu; Reming-Albert Yeh; Li-Hsin Shu; Yu-Ching Cheng; Hung Te Liu; Ching-Yuan Wu 2020 2020-03-26 BioRxiv Y 10.1101/2020.03.26.009803 7w79zeib 0.385822 UNKNOWN_1987, Callison_1999, Smith_2003, Ivarsson_2012 Yuan_2004, Veiga_2006
64 Langosch_2011 Helix-helix interaction patterns in membrane proteins Langosch, Dieter; Herrmann, Jana R.; Unterreitmeier, Stephanie; Fuchs, Angelika 2011 2011-01-04 PMC N PMC7123687 10.1007/978-3-7091-0045-5_10 mat3vf3r 0.384373 Ivarsson_2012, Smith_2003, Deng_2008 MacKenzie_2008, Chang_2008
65 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 0.380838
66 Scrima_2006 Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element Scrima, Andrea; Wittinghofer, Alfred 2006 2006-06-08 PMC N PMC1500855 16763562.0 10.1038/sj.emboj.7601171 gujr2fno 0.370668 Smith_2003, Ivarsson_2012 Myllykoski_2017, Kanitz_2019
67 Bongini_2020 A possible strategy to fight COVID-19: Interfering with spike glycoprotein trimerization Bongini, Pietro; Trezza, Alfonso; Bianchini, Monica; Spiga, Ottavia; Niccolai, Neri 2020 2020-04-09 PMC Y 10.1016/j.bbrc.2020.04.007 cqx306yh 0.366972 Ivarsson_2012, Gomis-Rüth_2003, Li_F_2016 Guillén_2009, Yuan_2004
68 Claridge_2009 A picornaviral loop-to-loop replication complex Claridge, Jolyon K.; Headey, Stephen J.; Chow, John Y.H.; Schwalbe, Martin; Edwards, Patrick J.; Jeffries, Cy M.; Venugopal, Hariprasad; Trewhella, Jill; Pascal, Steven M. 2009 2009-06-30 PMC N 19268541.0 10.1016/j.jsb.2009.02.010 fft1brwz 0.361836 Chan_2016
69 Manepalli_2012 Monoamine Transporter Structure, Function, Dynamics, and Drug Discovery: A Computational Perspective Manepalli, Sankar; Surratt, Christopher K.; Madura, Jeffry D.; Nolan, Tammy L. 2012 2012-08-24 PMC N PMC3475841 22918625.0 10.1208/s12248-012-9391-0 n3kjcm6s 0.360754 Liu_Z_2008, Ivarsson_2012
70 Maltas_2014 Binding interactions of niclosamide with serum proteins Maltas, Esra 2014 2014-12-31 PMC N PMC7129377 28911473.0 10.1016/j.jfda.2014.03.004 mmafv2b5 0.357078 Langosch_2011, Chan_2016, Ivarsson_2012, Kinjo_2012 Guo_L_2015, Moulaei_2010
71 Crone_2020 Modulation of Coiled-Coil Binding Strength and Fusogenicity through Peptide Stapling Crone, Niek S.\nA.; Kros, Alexander; Boyle, Aimee L. 2020 2020-02-14 PMC N PMC7086394 32058706.0 10.1021/acs.bioconjchem.0c00009 w61sqy17 0.352903 Ivarsson_2012, UNKNOWN_1987, Smith_2003, Wang_2014, Gomis-Rüth_2003 D’Errico_2009, Moulaei_2010
72 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 0.352896 Langosch_2011, Ivarsson_2012, Deng_2008 Moulaei_2010, Robinson_2013
73 Ku_T_2019 Synthesis of distal and proximal fleximer base analogues and evaluation in the nucleocapsid protein of HIV-1 Ku, Therese; Lopresti, Natalie; Shirley, Matthew; Mori, Mattia; Marchant, Jan; Heng, Xiao; Botta, Maurizio; Summers, Michael F.; Seley-Radtke, Katherine L. 2019 2019-07-01 PMC N 31126822.0 10.1016/j.bmc.2019.05.019 7cm6m1ol 0.352884
74 Antunes_2018 General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept Antunes, Dinler A.; Devaurs, Didier; Moll, Mark; Lizée, Gregory; Kavraki, Lydia E. 2018 2018-03-12 COMM-USE N PMC5847594 29531253.0 10.1038/s41598-018-22173-4 f6vsr6ia 0.352429 Liu_Z_2008, Ivarsson_2012 Park_2013
75 Prabakaran_2004 A model of the ACE2 structure and function as a SARS-CoV receptor Prabakaran, Ponraj; Xiao, Xiaodong; Dimitrov, Dimiter S 2004 2004-01-30 PMC N PMC7117316 14715271.0 10.1016/j.bbrc.2003.12.081 yvbsvalz 0.351972 UNKNOWN_1987, Ivarsson_2012, Callison_1999, Smith_2003 Zhang_2009, Guillén_2009
76 Pérez-Faginas_2011 Synthesis and SAR studies on azetidine-containing dipeptides as HCMV inhibitors Pérez-Faginas, Paula; Aranda, M. Teresa; García-López, M. Teresa; Snoeck, Robert; Andrei, Graciela; Balzarini, Jan; González-Muñiz, Rosario 2011 2011-02-01 PMC N PMC7127091 21256035.0 10.1016/j.bmc.2010.12.052 z6ijfhjp 0.351788 Smith_2003, Ivarsson_2012, Yang_2012, Deng_2006
77 Lin_P_2008 Correlation between dissociation and catalysis of SARS-CoV main protease Lin, Pei-Ying; Chou, Chi-Yuan; Chang, Hui-Chuan; Hsu, Wen-Chi; Chang, Gu-Gang 2008 2008-04-01 PMC N PMC7094404 18275836.0 10.1016/j.abb.2008.01.023 32c8lg9k 0.347805 Smith_2003, UNKNOWN_1987, Yang_2012 Tsai_2010
78 Acker_2011 Mechanism for Noncompetitive Inhibition by Novel GluN2C/D N-Methyl-d-aspartate Receptor Subunit-Selective Modulators Acker, Timothy M.; Yuan, Hongjie; Hansen, Kasper B.; Vance, Katie M.; Ogden, Kevin K.; Jensen, Henrik S.; Burger, Pieter B.; Mullasseril, Praseeda; Snyder, James P.; Liotta, Dennis C.; Traynelis, Stephen F. 2011 2011-08-01 PMC N PMC3198917 21807990.0 10.1124/mol.111.073239 7tkbh9k3 0.346520 Ivarsson_2012, Smith_2003, UNKNOWN_1987, Chang_2000
79 Smith_2003 Autoinhibition of Bcr-Abl through Its SH3 Domain Smith, Kristen M.; Yacobi, Rinat; Van Etten, Richard A. 2003 2003-07-31 PMC N PMC7128750 12887890.0 10.1016/s1097-2765(03)00274-0 8ksnihp6 0.340668 Ivarsson_2012
80 Mustafa_2019 Peptide-Protein Interaction Studies of Antimicrobial Peptides Targeting Middle East Respiratory Syndrome Coronavirus Spike Protein: An In Silico Approach Mustafa, Sabeena; Balkhy, Hanan; Gabere, Musa 2019 2019-07-01 COMM-USE N PMC6634063 31354813.0 10.1155/2019/6815105 w9a4gjv1 0.336470 Ivarsson_2012 Guillén_2009, Choy_2004
81 Miknis_2010 Crystal Structure of Human Interferon-λ1 in Complex with Its High-Affinity Receptor Interferon-λR1 Miknis, Zachary J.; Magracheva, Eugenia; Li, Wei; Zdanov, Alexander; Kotenko, Sergei V.; Wlodawer, Alexander 2010 2010-12-10 PMC N PMC2991516 20934432.0 10.1016/j.jmb.2010.09.068 7kd2ncb9 0.333368 Ivarsson_2012, Smith_2003, UNKNOWN_1987
82 Lee-Huang_2007 Discovery of small-molecule HIV-1 fusion and integrase inhibitors oleuropein and hydroxytyrosol: Part I. Integrase inhibition Lee-Huang, Sylvia; Huang, Philip Lin; Zhang, Dawei; Lee, Jae Wook; Bao, Ju; Sun, Yongtao; Chang, Young-Tae; Zhang, John; Huang, Paul Lee 2007 2007-03-23 None N PMC2790717 17275783.0 10.1016/j.bbrc.2007.01.071 19qg6uji 0.333368 Gomis-Rüth_2003, UNKNOWN_1987
83 Ziółkowska_2007 Crystallographic, thermodynamic, and molecular modeling studies of the mode of binding of oligosaccharides to the potent antiviral protein griffithsin Ziółkowska, Natasza E.; Shenoy, Shilpa R.; O'Keefe, Barry R.; McMahon, James B.; Palmer, Kenneth E.; Dwek, Raymond A.; Wormald, Mark R.; Wlodawer, Alexander 2007 2007-03-05 PMC N PMC7167611 17340634.0 10.1002/prot.21336 33qd2gpm 0.328044 Ivarsson_2012, Chan_2016, Gomis-Rüth_2003, Snyder_2005
84 Shulman-Peleg_2004 Recognition of Functional Sites in Protein Structures Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J. 2004 2004-06-04 PMC N PMC7126412 15147845.0 10.1016/j.jmb.2004.04.012 66qoykl1 0.322199 Liu_Z_2008 Kuhn_2006, Myllykoski_2017, Ziółkowska_2006
85 Ibrahim_2020 COVID-19 spike-host cell receptor GRP78 binding site prediction Ibrahim, Ibrahim M.; Abdelmalek, Doaa H.; Elshahat, Mohammed E.; Elfiky, Abdo A. 2020 2020-05-31 PMC Y 32169481.0 10.1016/j.jinf.2020.02.026 j10308i3 0.317902 Ivarsson_2012, UNKNOWN_1987, Smith_2003, Chan_2016 Shajahan_2020, Guillén_2009
86 Desautels_2020 Rapid in silico design of antibodies targeting SARS-CoV-2 using machine learning and supercomputing Thomas Desautels; Adam Zemla; Edmond Lau; Magdalena Franco; Daniel Faissol 2020 2020-04-10 BioRxiv Y 10.1101/2020.04.03.024885 kg2j0dqy 0.312269 Liu_Z_2008
87 Vicente_2015 Conformational changes of the HsDHODH N-terminal Microdomain via DEER Spectroscopy Vicente, Eduardo F.; Sahu, Indra D.; Costa-Filho, Antonio J.; Cilli, Eduardo M.; Lorigan, Gary A. 2015 2015-07-02 PMC N PMC4814773 26086954.0 10.1021/acs.jpcb.5b01706 j7g4obni 0.311839 Ivarsson_2012, UNKNOWN_1987, UNKNOWN_1993, Smith_2003 Myllykoski_2017
88 Villullas_2007 Mutational analysis of human CEACAM1: the potential of receptor polymorphism in increasing host susceptibility to bacterial infection Villullas, Silvia; Hill, Darryl J; Sessions, Richard B; Rea, Jon; Virji, Mumtaz 2007 2007-02-01 PMC N PMC1859983 16953805.0 10.1111/j.1462-5822.2006.00789.x 9zmyojbu 0.307309 Ivarsson_2012, Callison_1999, UNKNOWN_1987, Yang_2012 Bos_M_1999
89 Bissaro_2020 Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules? Bissaro, Maicol; Sturlese, Mattia; Moro, Stefano 2020 2020-02-27 COMM-USE N PMC7057144 32175307.0 10.3389/fchem.2020.00107 i2mac4xm 0.302031 Liu_Z_2008, Ivarsson_2012 Moulaei_2010, Kanitz_2019, Wang_2013