| |
original article |
Date |
Title |
Authors Max. 6 Authors |
| 1 |
[GO] |
2024―Mar―16 |
Testing the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein |
Pranav Garg, Shawn C.C. Hsueh, Steven S. Plotkin |
| 2 |
[GO] |
2024―Feb―08 |
A search for anti-SARS-CoV-2 compounds for the treatment of COVID-19 infection using chemical similarity analysis |
Siwar Khasawneh, Roshan Paudel |
| 3 |
[GO] |
2024―Feb―08 |
Cardiac pathophysiology of COVID-19 mediated by ryanodine receptor type 2 Ca2+ leak |
Laith Bahlouli, Steven Reiken, Haikel Dridi, Andrew R. Marks |
| 4 |
[GO] |
2024―Feb―08 |
Comprehensive analysis of spike protein mutations in coronavirus subvariants reveals newly emerging change in mode of entry and establishment of infection in hosts |
Asmaa Awan, Roshan Paudel |
| 5 |
[GO] |
2024―Feb―08 |
SARS-CoV-2 nsp3 C-terminal region: Conserved beyond coronavirus with potential role in DMV pore formation |
Yulia Pustovalova, Alexandra Pozhidaeva, Jeffrey C. Hoch |
| 6 |
[GO] |
2024―Feb―08 |
SARS-CoV-2 binding to terminal sialic acid of gangliosides embedded in lipid membranes |
Geetanjali Negi |
| 7 |
[GO] |
2024―Feb―08 |
EPR spectroscopic characterization of the topology of SARS-CoV-2 envelope protein |
Andrew K. Morris, Gary A. Lorigan |
| 8 |
[GO] |
2024―Feb―08 |
CIS-mediated interactions of the SARS-CoV-2 frameshift RNA alter its conformations and affect function |
Lukas Pekarek, Matthias Zimmer, Anne-Sophie Gribling-Burrer, Patrick Bohn, Redmond P. Smyth, Neva Caliskan |
| 9 |
[GO] |
2024―Feb―08 |
Mitochondrial network physiology disruption during SARS-CoV-2 infection in human lung organoids |
Gillian McMahon, Zichen Wang, Hiroyuki Hakozaki, Paul Marchando, Cyna R. Shirazinejad, Yuichiro Iwamoto, Anna Ye, David Drubin, Matthew Akamatsu, Johannes Schöneberg |
| 10 |
[GO] |
2024―Feb―08 |
The role of heparin in spike SARS-CoV-2 infection: From a model for heparan sulfates to a starting structure for antivirals |
Giulia Paiardi, Maria Milanesi, Matheus Ferraz, Liv Zimmermann, Chiara Urbinati, Pasqua Oreste, Francesca Caccuri, Petr Chlanda, Marco Rusnati, Rebecca C. Wade |
| 11 |
[GO] |
2024―Feb―08 |
Synthesis and characterization of SARS-CoV-2 membrane protein |
Sara Anbir, Yuanzhong Zhang, Thomas E. Kuhlman, Michael E. Colvin, Ajay Gopinathan, Umar Mohideen, Roya Zandi, Joseph McTiernan, Michael Worcester, Siyu Li |
| 12 |
[GO] |
2024―Feb―08 |
The role of ATP hydrolysis and product release in the translocation mechanism of SARS-CoV-2 nsp13 |
Priti Roy, Monsurat M. Lawal, Martin McCullagh |
| 13 |
[GO] |
2024―Feb―08 |
Expanding our knowledge of the SARS-CoV-2 polyproteins: Structural and biochemical insights into the viral processing |
Ruchi Yadav, Valentine V. Courouble, Sanjay K. Dey, Jerry Joe E.K. Harrison, Jennifer Timm, Jesse B. Hopkins, Ryan L. Slack, Stefan G. Sarafianos, Francesc X. Ruiz, Patrick Griffin, Eddy Arnold |
| 14 |
[GO] |
2024―Feb―08 |
Structural insights into cross-reactive antibodies recognizing the N-terminal and receptor binding domains of the SARS-CoV-2 spike glycoprotein |
Adonis Rubio, Morgan Abernathy, Yu Erica Lee, Teresia Chen, Christopher O. Barnes |
| 15 |
[GO] |
2024―Feb―08 |
Novel SARS-CoV-2 VLP system and structural characterization by cryogenic electron tomography reveals orf3A and orf7A accessory proteins as critical for assembly |
Juliana Abramovich |
| 16 |
[GO] |
2024―Feb―08 |
Optimization and applications of a compact stem-loop DNA aptamer targeting SARS-CoV-2 nucleocapsid protein |
Morgan Esler, Christopher Belica, Arad Moghadasi, Ke Shi, Mackenzie Wyllie, Daniel A. Harki, Reuben S. Harris, Hideki Aihara |
| 17 |
[GO] |
2024―Feb―08 |
Structural restraints in the SARS-CoV-2 spike tail control its intra-cellular trafficking to virion assembly and immune presentation sites |
Syed Saif Hasan, Debajit Dey, Suruchi Singh, Enya Qing, Yanan He, Yihong Chen, Benjamin Jennings, Whitaker Cohn, Lokesh Gakhar, Nicholas J. Schnicker, Brian Pierce, Julian Whitelegge, Balraj Doray, John P. Orban, Tom Gallagher |
| 18 |
[GO] |
2024―Feb―08 |
Common cold coronavirus (CoV229E) infections alters 3D genomic architecture |
Ankush Singhal, Cullen Roth, Sofiya Micheva-Viteva, Vrinda Venu, Christina Steadman, Shawns Starkenburg, Karissa Y. Sanbonmatsu |
| 19 |
[GO] |
2024―Feb―08 |
Adsorption of pulmonary surfactants on the spike proteins of SARS-CoV-2 and its variants |
Kolattukudy P. Santo, Ryan Jaworski, Alexander Neimark |
| 20 |
[GO] |
2024―Feb―08 |
The effect of lipid and protein flexibility on membrane deformations caused by the SARS-CoV-2 E protein |
Jesse W. Sandberg, Grace H. Brannigan |
| 21 |
[GO] |
2024―Feb―08 |
Flipped over u: Structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease |
Meredith N. Frazier, Monica Pillon, Lucas Dillard, Juno Krahn, Isha Wilson, Jason Williams, Lalith Perera, Kevin John Butay, Leesa Deterding, Mario J. Borgnia, Robin Stanley |
| 22 |
[GO] |
2024―Feb―08 |
The SARS-CoV-2 envelope protein channel displays weak selectivity and heterogeneous oligomerization |
Vicente M. Aguilella, Maria Queralt-Martin, Wahyu Surya, Ernesto Tavares Neto, Andrea Sanchis, Antonio Alcaraz, Jaume Torres |
| 23 |
[GO] |
2024―Feb―08 |
Investigating how the anionic lipid, BMP, plays a crucial role in the initation of SARS-CoV-2 fusion |
Daniel Birtles |
| 24 |
[GO] |
2024―Feb―08 |
Reversal of the fusion catalytic role of SARS-CoV-2 fusion peptide by restricting the N terminus: Implications to tackle viral infection |
Avijit Sardar, Tapas Bera, Santosh K. Samal, Samit Guha, Pradip K. Tarafdar |
| 25 |
[GO] |
2024―Feb―08 |
An efficient protocol for accurately triaging molecules in the development of a SARS-CoV-2 main protease inhibitor |
Alexander M. Payne, Benjamin Kaminow, John D. Chodera |
| 26 |
[GO] |
2024―Feb―08 |
Revealing membrane factors that control SARS-CoV-2 membrane fusion and entry kinetics |
Marcos Cervantes, Tobin Hess, Peter Kasson |
| 27 |
[GO] |
2024―Feb―08 |
Molecular dynamics simulations of the SARS-CoV-2 membrane protein and its implications for viral assembly |
Joseph McTiernan, Ajay Gopinathan, Michael E. Colvin |
| 28 |
[GO] |
2024―Feb―08 |
Interactions of SARS-CoV-2 nsp7 or nsp8 with nsp12 causes severe constriction of RNA entry channel: Implications for novel RdRp inhibitor drug discovery |
Deepa Singh, Tushar Kushwaha, Rajkumar Kulandaisamy, Vikas Kumar, Kamal Baswal, Saras H. Tiwari, Arkadyuti Ghorai, Mohan B. Appaiahgari, Krishna K. Inampudi |
| 29 |
[GO] |
2024―Feb―08 |
DNA folding by SARS-CoV-2 nucleocapsid protein |
Jonathan Xing, Youna J. Choi, Ashley Carter |
| 30 |
[GO] |
2024―Feb―08 |
Single-molecule spectroscopy of the SARS-CoV-2 nucleocapsid protein |
Jasmine Cubuk, J. Jeremias Incicco, Melissa D. Stuchell-Brereton, Kathleen B. Hall, Andrea Soranno |
| 31 |
[GO] |
2024―Feb―08 |
Phosphorylation regulates the function of the SARS-COV-2 nucleocapsid protein |
Bruna Favetta, Huan Wang, Mayur Barai, Bineet Sharma, Cesar Ramirez, Gabriela Tirado-Mansilla, Sanjeeva Murthy, Adam Gormley, Zheng Shi, Benjamin S. Schuster |
| 32 |
[GO] |
2024―Feb―08 |
Impact of crowding on conformations and interactions of the SARS-CoV-2 nucleocapsid protein and RNA |
Madison Stringer, Jasmine Cubuk, Jeremias Incicco, Debjit Roy, Kathleen B. Hall, Melissa D. Stuchell-Brereton, Andrea Soranno |
| 33 |
[GO] |
2024―Feb―08 |
The evolving biophysics and antigenicity of the SARS-CoV-2 Omicron spike receptor binding domain |
Jared Lindenberger, Chan Soo Park, Salam Sammour, Xiao Huang, Katarzyna Janowska, Priyamvada Acharya |
| 34 |
[GO] |
2024―Feb―08 |
Computational investigations of SARS-CoV-2 proofreading exoribonuclease (ExoN) suggest strategies for antiviral design |
Eleonora Gianti |
| 35 |
[GO] |
2024―Feb―08 |
Localization of viral RNA and proteins in the SARS-CoV-2 replication organelles revealed by super-resolution microscopy |
Leonid Andronov, Mengting Han, Yanyu Zhu, Anish R. Roy, Andrew E.S. Barentine, Lei S. Qi, William E. Moerner |
| 36 |
[GO] |
2024―Feb―08 |
Harnessing molecular simulations to design stabilized SARS-CoV-2 S2 antigens |
Lorenzo Casalino, Xandra Nuqui, Ling Zhou, Mohamed Shehata, Albert Wang, Alexandra L. Tse, Anupam A. Ojha, Fiona L. Kearns, Mia A. Rosenfeld, Emily H. Miller, Cory M. Acreman, Surl-Hee Ahn, Kartik Chandran, Jason S. McLellan, Rommie E. Amaro |
| 37 |
[GO] |
2024―Feb―08 |
Real-time visualization of intermolecular interactions between SARS-CoV-2 spike protein and NTD-binding antibody using high-speed atomic force microscopy |
Pangmiaomiao Zhang, Chia-Wei Chou, Ilya J. Finkelstein, Yi-Chih Lin |
| 38 |
[GO] |
2024―Feb―08 |
An implicit dye sampling technique for the study of conformational dynamics of SARS-CoV-2 spike protein variants |
Joseph Williamson, Maolin Lu, Mahmoud Moradi |
| 39 |
[GO] |
2024―Feb―08 |
Structures and stability of SARS-CoV-2 spike S2 subunit mutants targeting inter-subunit interactions |
Ruth J. Parsons, Alexandria Calloway, Ellie Zhang, Bhishem Thakur, Katarzyna Janowska, Priyamvada Acharya |
| 40 |
[GO] |
2024―Feb―08 |
Biophysical principles predict fitness of SARS-CoV-2 variants |
Dianzhuo Wang, Marian Huot, Vaibhav Mohanty, Eugene Shakhnovich |
| 41 |
[GO] |
2024―Feb―08 |
Role of the proton-activated chloride channel in SARS-CoV-2 viral entry |
Nicholas R.M. Koylass, Henry Yi Cheng, Kevin Chen, Zhaozhu Qiu |
| 42 |
[GO] |
2024―Feb―08 |
Host microRNA interactions with the SARS-COV-2 viral genome 3′-untranslated region |
Caleb J. Frye, Caylee Cunningham, Mihaela-Rita Mihailescu |
| 43 |
[GO] |
2024―Feb―08 |
Investigating spike S2 subunit hairpin proteins of the SARS-CoV-2 virus |
Noel Chau, Rob Wolfe, Gavin Engweiler, David P. Weliky |
| 44 |
[GO] |
2024―Feb―08 |
Cooperativity and induced oligomerization control the interaction of SARS-CoV-2 with its cellular receptor and patient-derived antibodies |
Roi Asor, Anna Olerinyova, Sean A. Burnap, Manish S. Kushwah, Mario Hensen, Snežana Vasiljevic, Liu Chang, Wanwisa Dejnirattisa, Piyada Supasa, David I. Stuart, Gavin R. Screaton, Nicole Zitzmann, Justin L.P. Benesch, Weston B. Struwe, Philipp Kukura |
| 45 |
[GO] |
2024―Feb―08 |
Capturing the biomechanics of SARS-COV-2/antibody complexes by GōMartini simulation |
Luis F. Cofas-Vargas, Adolfo Poma |
| 46 |
[GO] |
2024―Jan―17 |
Targeting protein-protein interaction interfaces with anti-viral N protein inhibitor in SARS-CoV-2 |
Jhen-Yi Hong, Shih-Chao Lin, Kylene Kehn-Hall, Kai-Min Zhang, Shun-Yuan Luo, Hung-Yi Wu, Sui-Yuan Chang, Ming-Hon Hou |
| 47 |
[GO] |
2023―Oct―28 |
Biophysical evolution of the receptor binding domains of SARS-CoVs |
Vaibhav Upadhyay, Sudipta Panja, Alexandra Lucas, Casey Patrick, Krishna M.G. Mallela |
| 48 |
[GO] |
2023―Sep―16 |
Structure adaptation in Omicron SARS-CoV-2/hACE2: Biophysical origins of evolutionary driving forces |
Ya-Wen Hsiao, David J. Bray, Tseden Taddese, Guadalupe Jiménez-Serratos, Jason Crain |
| 49 |
[GO] |
2023―Mar―24 |
Loading dynamics of one SARS-CoV-2-derived peptide into MHC-II revealed by kinetic models |
Kaiyuan Song, Honglin Xu, Lin-Tai Da |
| 50 |
[GO] |
2023―Feb―15 |
Conformational Ensemble of the NSP1 CTD in SARS-Cov2: Perspectives from the Free Energy Landscape |
Pallab Dutta, Abhay Kshirsagar, Parth Bibekar, Neelanjana Sengupta |
| 51 |
[GO] |
2023―Feb―10 |
Molecular mechanisms of cardiac complications associated with COVID-19 |
Steven R. Reiken, Haikel Dridi, Leah Sittenfeld, Yang Liu, Andrew R. Marks |
| 52 |
[GO] |
2023―Feb―10 |
SARS-CoV-2 spike protein-induced inflammation underlies proarrhythmia in COVID-19 |
Louisa Mezache, Gerard Nuovo, David Suster, Esmerina Tili, Hamdy Awad, Przemyslaw Radwanski, Rengasayee Veeraraghavan |
| 53 |
[GO] |
2023―Feb―10 |
Three-dimensional chromatin ensemble reconstruction via stochastic embedding reveals a missing link from COVID-19 infection to anosmia |
Igor N. Berezovsky |
| 54 |
[GO] |
2023―Feb―10 |
Comparison of three mathematical models for COVID-19 prediction |
Pelayo Martınez Fernandez, Zulima Fernandez-Muniz, Ana Cernea, Juan Luis Fernandez-Martınez, Andrzej Kloczkowski |
| 55 |
[GO] |
2023―Feb―10 |
Elucidating coronavirus fusion mechanisms |
Tobin Hess, Marcos Cervantes, Anjali Sengar, Peter Kasson |
| 56 |
[GO] |
2023―Feb―10 |
Polymer modelling accurately predicts three-dimensional chromosome reorganization with a seasonal coronavirus infection |
Ankush Singhal, Cullen Roth, Sofiya Micheva-Viteva, Anna Lappala, Jeannie T. Lee, Shawn R. Starkenburg, Karissa Y. Sanbonmatsu |
| 57 |
[GO] |
2023―Feb―10 |
Multicolor super-resolution imaging to study human coronavirus RNA during cellular infection |
Anish R. Roy, Jiarui Wang, Mengting Han, Haifeng Wang, Leonhard Möckl, Leiping Zeng, William E. Moerner, Lei S. Qi |
| 58 |
[GO] |
2023―Feb―10 |
Natural effectors for conformational control of coronavirus spike proteins |
Daniel Asarnow, David Veesler |
| 59 |
[GO] |
2023―Feb―10 |
Analysis of the conserved and mutated amino acid sequences in the spike protein enhances the understanding of phylognetic relationship among coronavirus variants from the wild type |
Asmaa Awan, Roshan Paudel |
| 60 |
[GO] |
2023―Feb―10 |
Integration of smFRET and molecular dynamics to characterize conformational dynamics of the spike protein of wild-type SARS-CoV-2 and its variants |
Joseph Williamson, Maolin Lu, Mahmoud Moradi |
| 61 |
[GO] |
2023―Feb―10 |
Ascertaining mesoscopic parameters for SARS-CoV-2 assembly from all atom and coarse-grained simulations of the associated membrane protein |
Joseph McTiernan, Ajay Gopinathan, Michael E. Colvin |
| 62 |
[GO] |
2023―Feb―10 |
Understanding the mechanisms of increased pathogenicity and virulence of SARS-CoV-2 Delta and Omicron variants |
Mandira Dutta, Gregory A. Voth |
| 63 |
[GO] |
2023―Feb―10 |
Comparing elastic and molecular models of membrane bending local to SARS-CoV-2 envelope protein for mechanistic understanding |
Jesse W. Sandberg, Grace H. Brannigan |
| 64 |
[GO] |
2023―Feb―10 |
Ion channels activity of SARS-CoV-2 envelope protein through calcium influx assay using large unilamellar vesicles |
Hyejin Jeong |
| 65 |
[GO] |
2023―Feb―10 |
Identification and characterization of E266Q mutation in Nsp15 endoribonuclease from SARS-CoV-2 Epsilon variant |
Manashi Sonowal, Nirupa Nagaratnam, Rebecca J. Jernigan, Dhenugen Logeswaran, Raimund Fromme, Julian J.-L. Chen, Petra Fromme |
| 66 |
[GO] |
2023―Feb―10 |
The SARS-CoV-2 fusion domain preferentially initiates fusion in the late endosome |
Daniel Birtles, Jinwoo Lee |
| 67 |
[GO] |
2023―Feb―10 |
Single-molecule assay for highly sensitive SARS-CoV-2 gene detection based on CRISPR-Cas12a |
Sangmin Ji, Hye Ran Koh |
| 68 |
[GO] |
2023―Feb―10 |
Structure of SARS-CoV-2 M protein in lipid nanodiscs |
Kimberly A. Dolan, Mandira Dutta, David Kern, Abhay Kotecha, Gregory A. Voth, Steve Brohawn |
| 69 |
[GO] |
2023―Feb―10 |
Computational fragment screening of dimeric SARS-CoV-2 main protease |
Rashad L. Reid, Vincent Voelz |
| 70 |
[GO] |
2023―Feb―10 |
The conformational space of the SARS-CoV-2 main protease active site loops is determined by ligand binding and interprotomer allostery |
Ethan Lee, Sarah Rauscher |
| 71 |
[GO] |
2023―Feb―10 |
A genetically encoded BRET-based SARS-CoV-2 main protease activity sensor |
Anupriya M. Geethakumari, Wesam S. Ahmed, Saad Rasool, Asma Fatima, S. M. Nasir Uddin, Mustapha Aouida, Kabir H. Biswas |
| 72 |
[GO] |
2023―Feb―10 |
Dynamics of the SARS-CoV-2 main protease binding site |
Advaith S. Harith, Sacha Mallalieu, Amelia A. Fuller, Michelle E. McCully |
| 73 |
[GO] |
2023―Feb―10 |
Inhibition of the SARS-CoV-2 main protease by a thiadiazolidinone derivative |
Katarina Jovic, Logan Brown, Harish Vashisth, Krisztina Varga |
| 74 |
[GO] |
2023―Feb―10 |
Small molecule co-solvents enhance activity of SARS-CoV-2 main protease through a dielectric effect |
Marquise G. Crosby |
| 75 |
[GO] |
2023―Feb―10 |
Drug discovery targeting SARS-CoV-2 membrane fusion |
Kailu Yang, Chuchu Wang, Alex J.B. Kreutzberger, Ravi Ojha, Suvi Kuivanen, Sergio Couoh-Cardel, Serena Muratcioglu, Timothy J. Eisen, K. Ian White, Richard Pfuetzner, John Kuriyan, Olli Vapalahti, Giuseppe Balistreri, Tomas Kirchhausen, Axel T. Brunger |
| 76 |
[GO] |
2023―Feb―10 |
Identifying and sampling conformational states of SARS-CoV-2 mpro for flexible receptor docking |
Matthew S. Smith, Michael Grabe, Brian Shoichet |
| 77 |
[GO] |
2023―Feb―10 |
Studies on antiviral resistant SARS-CoV-2 Mpro mutants |
Morgan A. Esler, Arad Moghadasi, Reuben S. Harris, Hideki Aihara |
| 78 |
[GO] |
2023―Feb―10 |
SARS-CoV-2 Nsp3 oligomerization is a driver for molecular pore formation |
Yulia Pustovalova, Alexandra Pozhidaeva, Jeffrey C. Hoch |
| 79 |
[GO] |
2023―Feb―10 |
Dual functions of the SARS-CoV-2 nucleocapsid domains mediate RNA binding and phase separation |
Aidan B. Estelle, Zhen Yu, Patrick Allen, Elisar J. Barbar |
| 80 |
[GO] |
2023―Feb―10 |
Measuring DNA folding by the SARS-CoV-2 nucleocapsid protein |
Jake J. Kim, Youna N. Choi, Ashley R. Carter |
| 81 |
[GO] |
2023―Feb―10 |
Single-molecule spectroscopy of the SARS-CoV-2 nucleocapsid protein |
Jasmine Cubuk, Jeremias Incicco, Jhullian J. Alston, Kathleen B. Hall, Melissa D. Stuchell-Brereton, Andrea Soranno |
| 82 |
[GO] |
2023―Feb―10 |
Structure and function of SARS-CoV-2 nucleocapsid protein measured using optical tweezers, confocal fluorescence, and AFM |
Michael Morse, Jana Sefcikova, Micah J. McCauley, Ioulia F. Rouzina, Penny J. Beuning, Mark C. Williams |
| 83 |
[GO] |
2023―Feb―10 |
Combining simulations and single-molecule fluorescence spectroscopy to understand SARS-CoV-2 nucleocapsid protein RNA interaction |
Jhullian J. Alston, Jasmine Cubuk, Jeremias Incicco, Melissa D. Stuchell-Brereton, Kathleen B. Hall, Alex S. Holehouse, Andrea Soranno |
| 84 |
[GO] |
2023―Feb―10 |
Phase separation underlies interactions of the SARS-CoV-2 nucleocapsid protein with nucleoli |
Priyanka Dogra, Hazheen Shirnekhi, Mylene C. Ferrolino, Michele Tolbert, Cheon-Gil Park, Richard W. Kriwacki |
| 85 |
[GO] |
2023―Feb―10 |
The unique q493r mutation drives interfacial interactions in the SARS-CoV-2 Omicron variant S1-RBD: ACE2-complex |
Angelin M. Philip |
| 86 |
[GO] |
2023―Feb―10 |
Mechanism of assembly of an elongation-competent SARS-CoV-2 replication transcription complex |
Misha Klein, Subhas C. Bera, Thomas K. Anderson, Bing Wang, Flavia S. Papini, Jamie J. Arnold, Craig E. Cameron, Martin Depken, Robert N. Kirchdoerfer, Irina Artsimovitch, David Dulin |
| 87 |
[GO] |
2023―Feb―10 |
Structural and thermodynamic consequences of the G31U and U5C mutations in the SARS-CoV-2 s2m |
Adam H. Kensinger, Joseph A. Makowski, Kendy A. Pellegrene, Caylee L. Cunningham, Caleb J. Frye, Patrick E. Lackey, Mihaela-Rita Mihailescu, Jeffrey D. Evanseck |
| 88 |
[GO] |
2023―Feb―10 |
Delta variant versus ancestral SARS-CoV-2 s2m dynamics and relative entropy |
Joseph A. Makowski, Adam H. Kensinger, Kendy A. Pellegrene, Caylee Cunningham, Caleb J. Frye, Patrick E. Lackey, Mihaela-Rita Mihailescu, Jeffrey D. Evanseck |
| 89 |
[GO] |
2023―Feb―10 |
The molecular basis for dysfunctional bacterial lipopolysaccharide-mediated immune receptor activation by SARS-CoV-2 spike |
Firdaus Samsudin, Venkata Raghuvamsi Palur, Ganna Petruk, Manoj Puthia, Jitka Petrlova, Paul MacAry, Ganesh S. Anand, Artur Schmidtchen, Peter J. Bond |
| 90 |
[GO] |
2023―Feb―10 |
Post-translational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors |
Tianle Chen, Karan Kapoor, Emad Tajkhorshid |
| 91 |
[GO] |
2023―Feb―10 |
SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact |
Yui Tik Pang, Atanu Acharya, Diane L. Lynch, Anna Pavlova, James C. Gumbart |
| 92 |
[GO] |
2023―Feb―10 |
Single-molecule studies of RNA aptamers binding to SARS-CoV-2 spike proteins expressed on virus-like particles |
Brett Israels, Aleksandra Bednarz, Julian Valero Molero, Laia Civit Pitarch, Daniel Dupont, Mette Malle, Jorgen Kjems, Victoria Birkedal |
| 93 |
[GO] |
2023―Feb―10 |
Stabilized SARS-CoV-2 spike S2 immunogens designed using insights from enhanced sampling molecular dynamics simulations |
Xandra Nuqui, Lorenzo Casalino, Mohamed Shehata, Anupam A. Ojha, Fiona L. Kearns, Mia Rosenfeld, Jason S. McLellan, Rommie E. Amaro |
| 94 |
[GO] |
2023―Feb―10 |
Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants |
Eric Wang, Arup K. Chakraborty |
| 95 |
[GO] |
2023―Feb―10 |
Timeline of changes in spike conformational dynamics in emergent SARS-CoV-2 variants reveal progressive stabilization of trimer stalk and enhanced NTD dynamics |
Ganesh S. Anand, Sean Braet, Theresa Buckley, Varun Venkatakrishnan, Kim-Marie Dam, Pamela J. Bjorkman |
| 96 |
[GO] |
2023―Feb―10 |
Viral-host RNA-RNA interactions in SARS-CoV-2: Study of miR-34a-5p binding interactions within the genome 3'-untranslated region |
Caleb J. Frye, Caylee Cunningham, Adam H. Kensinger, Joseph A. Makowski, Jeffrey D. Evanseck, Mihaela-Rita Mihailescu |
| 97 |
[GO] |
2023―Jan―16 |
Interactions of SARS-CoV-2 and MERS-CoV Fusion Peptides Measured Using Single Molecule Force Methods |
Cindy Qiu, Gary R. Whittaker, Samuel H. Gellman, Susan Daniel, Nicholas L. Abbott |
| 98 |
[GO] |
2022―Nov―17 |
Structural Effects of Spike Protein D614G Mutation in SARS-CoV-2 |
Hisham M. Dokainish, Yuji Sugita |
| 99 |
[GO] |
2022―Aug―28 |
Circulating cell clusters aggravate the hemorheological abnormalities in COVID-19 |
Elahe Javadi, He Li, Ander Dorken Gallastegi, Galit H. Frydman, Safa Jamali, George Em Karniadakis |
| 100 |
[GO] |
2022―May―20 |
Finite element modeling of alpha-helices and tropocollagen molecules with reference to the spike of SARS-CoV-2 |
Tomasz Wierzbicki, Yuanli Bai |
| 101 |
[GO] |
2022―Apr―07 |
Role of spatial patterning of N-protein interactions in SARS-CoV-2 genome packaging |
Ian Seim, Christine A. Roden, Amy S. Gladfelter |
| 102 |
[GO] |
2022―Apr―02 |
Modeling insights into SARS-CoV-2 respiratory tract infections prior to immune protection |
Alexander Chen, Timothy Wessler, Katherine Daftari, Kameryn Hinton, Richard C. Boucher, Raymond Pickles, Ronit Freeman, Samuel K. Lai, M. Gregory Forest |
| 103 |
[GO] |
2022―Feb―11 |
Developing drugs against essential proteins of SARS-CoV-2 for the treatment of COVID-19 |
Teena Bajaj |
| 104 |
[GO] |
2022―Feb―11 |
Predictive mathematical models of the growth of the COVID-19 pandemic |
Juan Luis Fernández-Martínez, Zulima Fernández-Muñiz, Ana Cernea, Andrzej Kloczkowski |
| 105 |
[GO] |
2022―Feb―11 |
A year in the life of SARS-CoV-2 Mpro: molecular modeling and analysis of clinically observed Mpro variants from the first year of the COVID-19 pandemic |
Elizabeth M. Diessner, Gemma R. Takahashi, Thomas J. Cross, Carter T. Butts, Rachel W. Martin |
| 106 |
[GO] |
2022―Feb―11 |
Catalytic function and substrate specificity of alpha and beta coronavirus papain-like proteases: targeting human NL63, SARS-CoV and SARS-CoV-2 (Covid-19) with designed inhibitors |
Mackenzie E. Chapman, Courtney M. Daczkowski, Arun K. Ghosh, Andrew D. Mesecar |
| 107 |
[GO] |
2022―Feb―11 |
Quantitative analysis of hypericin interaction with SARS-CoV 2 and with a model membrane |
Matteo Mariangeli, Eleonora Uriati, Chantal Usai, Andrea Mussini, Samira Jadavi, Silvia Dante, Claudio Canale, Ana Moreno, Pietro Delcanale, Stefania Abbruzzetti, Alberto Diaspro, Cristiano Viappiani, Paolo Bianchini |
| 108 |
[GO] |
2022―Feb―11 |
Structural dynamic changes in the SARS-CoV and SARS-CoV-2 S spike assemblies upon ACE2 activation |
Chengbo Chen, James B. Munro, Kelly K. Lee |
| 109 |
[GO] |
2022―Feb―11 |
Structural and dynamical impact of the two-nucleotide difference in sequence between SARS-CoV and SARS-CoV-2 s2m using molecular dynamics |
Adam H. Kensinger, Kendy A. Pellegrene, Joseph A. Makowski, Caylee L. Cunningham, Caleb J. Frye, Mihaela-Rita Mihailescu, Jeffrey D. Evanseck |
| 110 |
[GO] |
2022―Feb―11 |
Characterizing the roles of chemo-mechanical couplings in the differential behavior of SARS-CoV-1 and SARS-CoV-2 spike glycoprotein |
Ugochi H. Isu, Vivek Govind Kumar, Mortaza Derakhshani-Molayousefi, Adithya Polasa, Mahmoud Moradi |
| 111 |
[GO] |
2022―Feb―11 |
Automated refinement protocol to improve the quality of protein structures deposited in the protein data bank, applied to SARS-Cov-2 |
Joseph Farrell, Esmael J. Haddadian |
| 112 |
[GO] |
2022―Feb―11 |
Stem-loop II motif (s2m) structural and dynamical differences between SARS-CoV-2 and b.1.617.2 (Delta) variant |
Joseph A. Makowski, Adam H. Kensinger, Kendy A. Pellegrene, Caylee Cunningham, Caleb J. Frye, Morgan Shine, Izayah Bojanac, Patrick Lackey, Mihaela-Rita Mihailescu, Jeffrey D. Evanseck |
| 113 |
[GO] |
2022―Feb―11 |
The discovery of antivirals and novel targets for SARS-CoV-2 and EV-A71 |
Christina Haddad, Blanton S. Tolbert, Amanda E. Hargrove, Gary Brewer, Mei-Ling Li |
| 114 |
[GO] |
2022―Feb―11 |
Structural dynamics of prefusion spike protein of SARS-CoV-2 and its variants |
Mortaza Derakhshani-Molayousefi, Ugochi Isu, Mahmoud Moradi |
| 115 |
[GO] |
2022―Feb―11 |
SARS-CoV-2 antibodies specific to the mesa and inner side of spike protein receptor binding domain maintain high affinities for both D614G and b.1.351 variants |
Kan Li, Richard H.C. Huntwork, Gillian Q. Horn, Elizabeth Feeney, Kathryn M. Hastie, Haoyang Li, Vamseedhar Rayaprolu, Olmedillas Olmedillas, Sharon L. Schendel, Mark Heise, Ralph S. Baric, S. Munir Alam, Erica Ollmann Saphire, Georgia D. Tomaras, S. Moses Dennison |
| 116 |
[GO] |
2022―Feb―11 |
Characterization of the S2M G15U mutation associated with the SARS-CoV-2 delta variant |
Caylee L. Cunningham, Caleb J. Frye, Joshua A. Imperatore, Kendy A. Pellegrene, Adam H. Kensinger, Joseph A. Makowski, Morgan Shine, Patrick Lackey, Jeffrey D. Evanseck, Mihaela-Rita Mihailescu |
| 117 |
[GO] |
2022―Feb―11 |
Changes in the receptor-binding interface may cause immune evasion by the SARS-CoV-2 delta variant b.1.617.2 |
Prabin Baral, Nisha Bhattarai, Md Lokman Hossen, Vitalii Stebliankin, Bernard S. Gerstman, Giri Narasimhan, Prem P. Chapagain |
| 118 |
[GO] |
2022―Feb―11 |
Impact of mutations near the SARS-CoV-2 furin-cleavage site on viral infectivity |
Kien Nguyen, Srirupa Chakraborty, Pedro D. Manrique, Bette Korber, S. Gnanakaran |
| 119 |
[GO] |
2022―Feb―11 |
The spike-ACE2 interaction underlying SARS-CoV-2 infection and inhibition is enhanced by intermolecular cross linking |
Roi Asor, Anna Olerinyova, Manish S. Kushwah, Fabian Soltermann, Lucas Powell Rudden, SnezÌŒana Vasiljevic, Juliane Brun, Mario Hensen, Michelle Hill, Matteo Degiacomi, Nicole Zitzmann, Weston B. Struwe, Philipp Kukura |
| 120 |
[GO] |
2022―Feb―11 |
Computational investigation of glycosaminoglycan cofactors in SARS-CoV-2 infection dynamics |
Mia A. Rosenfeld, Fiona L. Kearns, Sang Hoon Kim, Lorenzo Casalino, Micah Papanikolas, Carlos Simmerling, Rommie E. Amaro, Ronit Freeman |
| 121 |
[GO] |
2022―Feb―11 |
Developing inhibitors of the SARS-CoV-2 main protease |
Christian Seitz, Vedran Markota, Terra Sztain-Pedone, Morgan Esler, Arad Moghadasi, Samantha Kennelly, Ozlem Demir, Hideki Aihara, Daniel A. Harki, Reuben Harris, J. Andrew McCammon, Rommie E. Amaro |
| 122 |
[GO] |
2022―Feb―11 |
Dimethyl sulfoxide (DMSO) affects activity of SARS-CoV-2 main protease |
Marquise G. Crosby, Gemma R. Takahashi, Rachel W. Martin, Elizabeth Diessner, Brenna Norton-Baker, Carter T. Butts |
| 123 |
[GO] |
2022―Feb―11 |
Comprehensive virtual screening of 4.8k flavonoids reveals novel insights into the allosteric inhibition of SARS-CoV-2 MPRO |
Ana Paula Vargas Ruiz, Gabriel Jiménez Avalos, Nicolás E. Delgado, Gustavo Olivos Ramírez, Patricia Sheen, Miguel Quiliano, Mirko Zimic |
| 124 |
[GO] |
2022―Feb―11 |
Binding and compaction function of structural domains of SARS-CoV-2 nucleocapsid (N) protein on a single stranded nucleic acid substrate |
Michael Morse, Jana Sefcikova, Ioulia Rouzina, Penny J. Beuning, Mark C. Williams |
| 125 |
[GO] |
2022―Feb―11 |
Characterizing nucleic acid interactions with the N-Terminal binding domain of the SARS-CoV-2 nucleocapsid protein |
Jasmine Cubuk, Juan J. Incicco, Melissa D. Stuchell-Brereton, Kathleen B. Hall, Andrea Soranno |
| 126 |
[GO] |
2022―Feb―11 |
SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA |
Amanda Jack, Luke Ferro, Michael J. Trnka, Eddie Wehri, Amrut Nadgir, Xammy Nguyenla, Douglas Fox, Katelyn Costa, Sarah Stanley, Julia Schaletzky, Ahmet Yildiz |
| 127 |
[GO] |
2022―Feb―11 |
Investigating SARS-CoV-2 ORF7a and BST-2 heterodimerization by molecular dynamics simulations |
Min-Kang Hsieh, Jeffery B. Klauda |
| 128 |
[GO] |
2022―Feb―11 |
Comparing structural ensembles with DiffNets helps explain the activation mechanism of the SARS-CoV-2 protein NSP16 |
Michael D. Ward |
| 129 |
[GO] |
2022―Feb―11 |
Cryo-electron tomography of in vivo reconstituted SARS-CoV-2 replication/transcription organelles |
Cosmo Z. Buffalo, James H. Hurley |
| 130 |
[GO] |
2022―Feb―11 |
Single molecule activity assay for SARS-CoV-2 RNA dependent RNA polymerase |
SangYoon Chung, Yazan Alhadid, Maya Segal, Jookyung Lee, Sergei Borukhov, Shimon Weiss |
| 131 |
[GO] |
2022―Feb―11 |
Probing remdesivir nucleotide analogue insertion to SARS-CoV-2 RNA dependent RNA polymerase in viral replication |
Moises E. Romero, Chunhong Long, Daniel La Rocco, Anusha M. Keerthi, Dajun Xu, Jin Yu |
| 132 |
[GO] |
2022―Feb―11 |
Molecular mechanism for conformational activation of SARS-CoV-2 RNA polymerase by nucleoside triphosphate |
Wen Ma, J. Andrew McCammon |
| 133 |
[GO] |
2022―Feb―11 |
SARS-CoV-2 S1 spike protein peptides inhibit alpha 7 nAChRs and are counteracted by a PAM at alpha 7 |
Joseph Farley, Jonathan B. Anderson |
| 134 |
[GO] |
2022―Feb―11 |
Decreased interfacial dynamics caused by the N501Y mutation in the SARS-Cov-2 s1 spike:ACE2 complex |
Wesam S. Ahmed, Angelin M. Philip, Kabir H. Biswas |
| 135 |
[GO] |
2022―Feb―11 |
A high throughput method for ensemble antibody affinity measurements for SARS-CoV-2 samples |
Gabrielle Kosoy, Abdul Karim, Phuong Nguyen, Mark Sangster, David Topham, Benjamin Miller |
| 136 |
[GO] |
2022―Feb―11 |
Probing key interactions between SARS-CoV-2 spike and heparan sulfate |
Fiona L. Kearns, Mia Rosenfeld, Sang Hoon Kim, Lorenzo Casalino, Micah Papanikolas, Carlos Simmerling, Ronit Freeman, Rommie E. Amaro |
| 137 |
[GO] |
2022―Feb―11 |
SARS-CoV-2 spike binding to ACE2 is stronger and longer ranged with glycans |
Yihan Huang, Bradley Harris, Shiaki Minami, Seongwon Jung, Priya Shah, Somen Nandi, Karen McDonald, Roland Faller |
| 138 |
[GO] |
2022―Feb―11 |
Conformational changes in SARS-CoV-2 spike from the delta variant enhances viral transmissibility |
Varun Venkatakrishnan, Sean Braet, Theresa Buckley, Ganesh S. Anand |
| 139 |
[GO] |
2022―Feb―11 |
Computational studies of the dynamics of SARS-CoV-2 spike, membrane, and nucleocapsid proteins |
Mandira Dutta, Gregory A. Voth |
| 140 |
[GO] |
2022―Feb―11 |
Concerted hinge motions in SARS-CoV-2 spike modulated by glycan-glycan and glycan-lipid interactions |
Karan Kapoor, Tianle Chen, Emad Tajkhorshid |
| 141 |
[GO] |
2022―Feb―11 |
Ensemble-based, glycan-dependent epitope analysis of SARS-CoV-2 spike protein |
Tianle Chen, Karan Kapoor, Emad Tajkhorshid |
| 142 |
[GO] |
2022―Feb―11 |
Computationally engineered ACE2 decoy binds with nanomolar affinity with the SARS-CoV-2 spike protein |
Mohammad S. Islam, Brandon Havranek, Erik Procko, Kui Chan |
| 143 |
[GO] |
2022―Feb―11 |
The roles of glycans in the SARS-CoV-2 spike protein |
Lorenzo Casalino, Rommie E. Amaro |
| 144 |
[GO] |
2022―Feb―11 |
Unraveling SARS-CoV-2 spike protein activation pathway reveals unprecedented cryptic pockets |
Hisham M. Dokainish, Suyong Re, Takaharu Mori, Chigusa Kobayashi, Jaewoon Jung, Yuji Sugita |
| 145 |
[GO] |
2022―Feb―11 |
Machine learning reveals the critical interactions for SARS-CoV-2 spike protein binding to ACE2 |
Anna Pavlova, Zijian Zhang, Atanu Acharya, Diane L. Lynch, Yui Tik Pang, Zhongyu Mou, Jerry M. Parks, Christophe J. Chipot, James C. Gumbart |
| 146 |
[GO] |
2022―Feb―11 |
Elucidating the distinct structural features of the SARS-CoV-2 spike protein fusion domain |
Daniel Birtles |
| 147 |
[GO] |
2022―Feb―11 |
Host cell membrane capture by the SARS-CoV-2 spike protein fusion intermediate |
Rui Su, Jin Zeng, Ben O'Shaughnessy |
| 148 |
[GO] |
2022―Feb―11 |
Impact of SARS-CoV-2 spike protein on α7 nicotinic acetylcholine receptor in cells |
Tommy S. Tillman, Yan Xu, Pei Tang |
| 149 |
[GO] |
2022―Feb―11 |
The SARS-CoV-2 spike protein reversibly samples an open-trimer conformation exposing novel epitopes |
Sophie R. Shoemaker, Shawn M. Costello, Helen T. Hobbs, Annalee W. Nguyen, Ching-Lin Hsieh, Jennifer A. Maynard, Jason S. McLellan, John E. Pak, Susan Marqusee |
| 150 |
[GO] |
2022―Feb―11 |
Intricacies of the SARS-CoV-2 spike transmembrane trimer organization |
Elena T. Aliper, Nikolay A. Krylov, Anton A. Polyansky, Roman G. Efremov |
| 151 |
[GO] |
2022―Feb―11 |
Whole-cell quantitative imaging of structural changes induced by SARS-CoV-2 using soft X-ray tomography |
Jian-Hua Chen, Valentina Loconte, Mirko Cortese, Axel Ekman, Mark A. Le Gros, Ralf Bartenschlager, Venera Weinhardt, Carolyn A. Larabell |
| 152 |
[GO] |
2022―Feb―11 |
AI-Driven prediction of binding trends of SARS-CoV-2 variants from atomistic simulations |
Sara Capponi, Shangying Wang, Erik Navarro, Simone Bianco |
| 153 |
[GO] |
2022―Feb―11 |
Differential interactions between human ACE2 and spike RBD of SARS-CoV-2 variants of concern |
Seonghan Kim, Yi Liu, Zewei Lei, Jeffrey Dicker, Yiwei Cao, Xiaohui Zhang, Wonpil Im |
| 154 |
[GO] |
2022―Feb―11 |
SARS-Cov-2 variants of concern decelerate the dynamics of spike open conformation as an evolutionary strategy |
Ziwei Yang, Yang Han, Shilei Ding, Andrés Finzi, Walther Mothes, Maolin Lu |
| 155 |
[GO] |
2022―Feb―11 |
Structure, dynamics and nanomechanics of wild-type and alpha-variant SARS-CoV-2 virions |
Dorottya Mudra, Balint Kiss, Zoltán Kis, Bernadett Pályi, Miklós Kellermayer |
| 156 |
[GO] |
2022―Feb―11 |
Development of a SARS-CoV-2 virus-like particle that performs as a direct cell entry reporter |
Elena Mekhedov, Matthias Garten, Glen Humphrey, Jennifer D. Petersen, Adriana E. Golding, Hang Waters, Joshua Zimmerberg |
| 157 |
[GO] |
2022―Feb―11 |
Preparation of SARS-CoV-2 VLP to study viral assembly, egress, and entry |
Jennifer D. Petersen, Glen Humphrey, Elena Mekhedov, Hang Waters, Joshua Zimmerberg |
| 158 |
[GO] |
2022―Feb―11 |
Expression of SARS-CoV-2-ORF3a protein induces cardiomyocyte damage |
Iuliia A. Polina, Yugene Guo, Michael W. Cypress, Elena G. Tolkacheva, Bong Sook Jhun, Jin O-Uchi |
| 159 |
[GO] |
2022―Feb―11 |
Viral-host RNA-RNA interactions in SARS-CoV-2: study of MIR-760-3p interactions with the genome 3'-untranslated region |
Caleb J. Frye, Caylee L. Cunningham, Kendy A. Pellegrene, Adam H. Kensinger, Joseph A. Makowski, Jeffrey D. Evanseck, Mihaela-Rita Mihailescu |
| 160 |
[GO] |
2022―Feb―11 |
A tethered ligand assay to probe SARS-CoV-2:ACE2 interactions |
Magnus S. Bauer, Sophia Gruber, Adina Hausch, Lukas F. Milles, Thomas Nicolaus, Leonard C. Schendel, Pilar López Navajas, Erik Procko, Daniel Lietha, Rafael C. Bernardi, Jan Lipfert, Hermann E. Gaub |
| 161 |
[GO] |
2022―Feb―11 |
Developing lectins as inhibitors of SARS-CoV2 |
Alex J. Guseman, Linda Murphy, Sham Nambulli, Fatema Bhinderwhala, Paul Duprex, Angela M. Gronenborn |
| 162 |
[GO] |
2021―Dec―18 |
Importance of Negatively Charged Residues in the Membrane Ordering Activity of SARS-CoV-1 and -2 Fusion Peptides |
Alex L. Lai, Jack H. Freed |
| 163 |
[GO] |
2021―Dec―07 |
SARS-Cov-2 Spike binding to ACE2 is stronger and longer ranged due to glycan interaction |
Yihan Huang, Bradley S. Harris, Shiaki A. Minami, Seongwon Jung, Priya S. Shah, Somen Nandi, Karen A. McDonald, Roland Faller |
| 164 |
[GO] |
2021―Nov―10 |
Modeling Coronavirus Spike Protein Dynamics: Implications for Immunogenicity and Immune Escape |
G. Kunkel, M. Madani, S.J. White, P.H. Verardi, A. Tarakanova |
| 165 |
[GO] |
2021―Oct―28 |
More pandemic reflections |
H. Jane Dyson |
| 166 |
[GO] |
2021―Jul―31 |
“Bucket brigade” using lysine residues in RNA-dependent RNA polymerase of SARS-CoV-2 |
Shoichi Tanimoto, Satoru G. Itoh, Hisashi Okumura |
| 167 |
[GO] |
2021―Jul―14 |
Biophysicists’ continued outstanding response to COVID-19 |
Tamar Schlick, Eric J. Sundberg, Susan J. Schroeder, M. Madan Babu |
| 168 |
[GO] |
2021―Jun―30 |
Role of spatial patterning of N-protein interactions in SARS-CoV-2 genome packaging |
Ian Seim, Christine A. Roden, Amy S. Gladfelter |
| 169 |
[GO] |
2021―Jun―29 |
Regulation of epithelial sodium channel activity by SARS-CoV-1 and SARS-CoV-2 proteins |
Stephen N. Grant, Henry A. Lester |
| 170 |
[GO] |
2021―Jun―29 |
Transient complexes of the Nsp7, Nsp8 and Nsp12 in SARS-CoV-2 replication transcription complex |
Mateusz Wilamowski, Michal Hammel, Wellington Leite, Qiu Zhang, Youngchang Kim, Kevin Weiss, Robert Jedrzejczak, Daniel J. Rosenberg, Yichong Fan, Jacek Wower, Jan Bierma, Altaf H. Sarker, Susan E. Tsutakawa, Sai Venkatesh Pingali, Hugh M. O’Neill, Andrzej Joachimiak, Greg L. Hura |
| 171 |
[GO] |
2021―Jun―29 |
Dynamics of the SARS-CoV-2 nucleoprotein N-terminal domain triggers RNA duplex destabilization |
Ícaro P. Caruso, Karoline Sanches, Andrea T. Da Poian, Anderson S. Pinheiro, Fabio C.L. Almeida |
| 172 |
[GO] |
2021―Jun―02 |
Physical phenotype of blood cells is altered in COVID-19 |
Markéta Kubánková, Bettina Hohberger, Jakob Hoffmanns, Julia Fürst, Martin Herrmann, Jochen Guck, Martin Kräter |
| 173 |
[GO] |
2021―Jun―02 |
Neuropilin-1 Assists SARS-CoV-2 Infection by Stimulating the Separation of Spike Protein Domains S1 and S2 |
Li Zhen-lu, Buck Matthias |
| 174 |
[GO] |
2021―Jun―02 |
Enhanced Sampling Protocol to Elucidate Fusion Peptide Opening of SARS-CoV-2 Spike Protein |
Jacob M. Remington, Kyle T. McKay, Jonathon B. Ferrell, Severin T. Schneebeli, Jianing Li |
| 175 |
[GO] |
2021―May―11 |
Computational optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2 |
Savvas Polydorides, Georgios Archontis |
| 176 |
[GO] |
2021―Mar―29 |
Multivalent binding of the partially disordered SARS-CoV-2 nucleocapsid phosphoprotein dimer to RNA |
Heather M. Forsythe, Joaquin Rodriguez Galvan, Zhen Yu, Seth Pinckney, Patrick Reardon, Richard B. Cooley, Phillip Zhu, Amber D. Rolland, James S. Prell, Elisar Barbar |
| 177 |
[GO] |
2021―Mar―29 |
SARS-CoV2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential |
Neha Vithani, Michael D. Ward, Maxwell I. Zimmerman, Borna Novak, Jonathan H. Borowsky, Sukrit Singh, Gregory R. Bowman |
| 178 |
[GO] |
2021―Mar―09 |
Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2 |
Mahdi Ghorbani, Bernard R. Brooks, Jeffery B. Klauda |
| 179 |
[GO] |
2021―Mar―04 |
Biophysicists' outstanding response to Covid-19 |
Tamar Schlick, Eric J. Sundberg, Susan J. Schroeder, M. Madan Babu |
| 180 |
[GO] |
2021―Mar―04 |
Principles and Practice for SARS-CoV-2 Decontamination of N95 Masks with UV-C |
Thomas Huber, Olivia Goldman, Alexander E. Epstein, Gianna Stella, Thomas P. Sakmar |
| 181 |
[GO] |
2021―Mar―04 |
Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane |
Defne Gorgun, Muyun Lihan, Karan Kapoor, Emad Tajkhorshid |
| 182 |
[GO] |
2021―Feb―23 |
Ca2+-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide |
George Khelashvili, Ambrose Plante, Milka Doktorova, Harel Weinstein |
| 183 |
[GO] |
2021―Feb―18 |
A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors |
A. Sofia F. Oliveira, Amaurys Avila Ibarra, Isabel Bermudez, Lorenzo Casalino, Zied Gaieb, Deborah K. Shoemark, Timothy Gallagher, Richard B. Sessions, Rommie E. Amaro, Adrian J. Mulholland |
| 184 |
[GO] |
2021―Feb―17 |
Biomechanical Characterization of SARS-CoV-2 Spike RBD and Human ACE2 Protein-Protein Interaction |
Wenpeng Cao, Chuqiao Dong, Seonghan Kim, Decheng Hou, Wanbo Tai, Lanying Du, Wonpil Im, X. Frank Zhang |
| 185 |
[GO] |
2021―Feb―12 |
Hydrating the Respiratory Tract: An Alternative Explanation Why Masks Lower Severity of COVID-19 |
Joseph M. Courtney, Ad Bax |
| 186 |
[GO] |
2021―Feb―12 |
Vitamin D and Its Derivatives as Promising Drugs Against COVID-19 - A Computational Study |
Yuwei Song, Shariq Qayyum, Radomir Slominski, Chander Raman, Andrzej Slominski, Yuhua Song |
| 187 |
[GO] |
2021―Feb―12 |
Rationally Designed Chimeric Antibodies for COVID-19 and Future Coronavirus Variants |
Ching-chung Hsueh, Steven S. Plotkin |
| 188 |
[GO] |
2021―Feb―12 |
COVID-19 Drugs Chloroquine and Hydroxychloroquine, but Not Azithromycin and Remdesivir, Block hERG Potassium Channels |
Mark Szendrey, Jun Guo, Wentao Li, Tonghua Yang, Shetuan Zhang |
| 189 |
[GO] |
2021―Feb―12 |
Investigational Treatments for COVID-19 May Increase Ventricular Arrhythmia Risk through Drug Interactions |
Meera Varshneya, Itziar Irurzun-Arana, Chiara Campana, Rafael Dariolli, Amy Gutierrez, Taylor K. Pullinger, Eric A. Sobie |
| 190 |
[GO] |
2021―Feb―12 |
Introductory Models of the Covid-19 Pandemic in the United States |
Peter H. Nelson |
| 191 |
[GO] |
2021―Feb―12 |
Identification of FDA Approved Antiviral Drugs for COVID-19 Treatment using Unbiased Virtual Screening |
Rory Greer, Yuwei Song, Michael J. Patton, Matthew Might, Kevin Harrod, Chad M. Petit, Yuhua Song |
| 192 |
[GO] |
2021―Feb―12 |
Coronavirus Envelope Protein: Lipid Sensitivity and Membrane Bending |
Jesse Sandberg, Grace H. Brannigan |
| 193 |
[GO] |
2021―Feb―12 |
Coronavirus Pathogenicity is Determined by Stability of the Spike Protein Open Conformation |
Josiah Bones, Ben Corry |
| 194 |
[GO] |
2021―Feb―12 |
Modeling and Manipulating Antibody Response Against Influenza and Coronavirus Spike Proteins and Exploring their Role in Directing Spike Evolution |
Assaf Amitai, Maya Sangesland, Daniel Lingwood, Arup K. Chakraborty |
| 195 |
[GO] |
2021―Feb―12 |
Anti-Frameshifting Ligand Active against SARS Coronavirus-2 is Resistant to Natural Mutations of the Frameshift-Stimulatory Pseudoknot |
Krishna Neupane, Sneha Munshi, Meng Zhao, Dustin Ritchie, Sandaru M. Ileperuma, Michael T. Woodside |
| 196 |
[GO] |
2021―Feb―12 |
Differential Dynamic Behavior of Prefusion Spike Glycoproteins of Sars Coronaviruses 1 and 2 |
Mahmoud Moradi, Vivek Govind Kumar, Dylan S. Ogden, Ugochi Isu, James Losey |
| 197 |
[GO] |
2021―Feb―12 |
Distinct Differences in the Interactions of Receptor Binding Domains of SARS-CoV-2 and SARS-CoV with Human ACE2 |
Atanu Acharya, Anna Pavlova, Christophe J. Chipot, James C. Gumbart |
| 198 |
[GO] |
2021―Feb―12 |
An Integrative MD Simulation and Network Analysis Approach to Study Glycosylation of Spike in SARS-CoV-2 |
Mahdi Ghorbani, Bernard R. Brooks, Jeffery B. Klauda |
| 199 |
[GO] |
2021―Feb―12 |
Combining Computational Modeling with Library Screening to Adapt SARS-CoV-Neutralizing Antibody 80R to SARS-CoV-2 |
Michael S. Kent, Maxwell Stefan, Kenneth Sale, Corey Hudson, Daniella Martinez, Miranda Juarros, Brooke Harmon, Daniel Gelperin, Valerie Duva, Alyssa Wynne, Valeria Busygina |
| 200 |
[GO] |
2021―Feb―12 |
Modeling Protein-Lipid Interactions during Viral Assembly of SARS-CoV-2 |
Viviana Monje-Galvan, Alexander Pak, Gregory A. Voth |
| 201 |
[GO] |
2021―Feb―12 |
Adaptive Evolution of Peptide Inhibitors for Mutating SARS-CoV-2 |
Parth Chaturvedi, Yanxiao Han, Petr Král, Lela Vukovic |
| 202 |
[GO] |
2021―Feb―12 |
Quantitative Fluorescence Microscopy on SARS-CoV-2 |
Rayna M. Addabbo, John Kohler, Isaac Angert, Yan Chen, Heather Hanson, Louis M. Mansky, Joachim D. Mueller |
| 203 |
[GO] |
2021―Feb―12 |
The Effect of Glycans Steric Potentials on Virus Infectivity- the SARS-Cov-2 Case |
Giuseppe Battaglia |
| 204 |
[GO] |
2021―Feb―12 |
Characterization of SARS-CoV-2 Conserved Elements’ Structures and their RNA-RNA Interactions |
Caylee Cunningham, Joshua Imperatore, Ella Milback, Morgan Shine, Kendy A. Pellegrene, Patrick Lackey, Jeffrey D. Evanseck, Mihaela-Rita Mihailescu |
| 205 |
[GO] |
2021―Feb―12 |
Structural Dynamics of SARS-CoV-2 Frameshift Signal Studied by Single-Molecule Force Spectroscopy Reveal Topologically Distinct Conformers |
Krishna P. Neupane, Meng Zhao, Noel Q. Hoffer, Aaron Lyons, Sneha Munshi, Dustin Ritchie, Michael T. Woodside |
| 206 |
[GO] |
2021―Feb―12 |
High-Coverage Nucleic Acid Probes for Distinguishing SARS-COV-2 from Influenza |
Samantha J. Courtney, Zachary R. Stromberg, James Theiler, Brian T. Foley, Jason D. Gans, Karina Yusim, Jessica Z. Kubicek-Sutherland |
| 207 |
[GO] |
2021―Feb―12 |
The Design of a Destabilizer Peptide to Disrupt SARS-CoV-2 Fusion with Its Targeted Cell Membrane |
Motamed Qadan |
| 208 |
[GO] |
2021―Feb―12 |
SARS-CoV-2 Glycosylated Spike Activation Mechanism - Simulations of the Full Unbiased Pathway |
Terra Sztain-Pedone, Surl-Hee Ahn, Anthony Bogetti, Lorenzo Casalino, Zied Gaieb, James A. McCammon, Lillian T. Chong, Rommie E. Amaro |
| 209 |
[GO] |
2021―Feb―12 |
Inhibitor Binding Influences the Protonation State of Histidines in SARS-CoV-2 Main Protease |
Anna Pavlova, Diane L. Lynch, Micholas Dean Smith, Jeremy D. Smith, James C. Gumbart |
| 210 |
[GO] |
2021―Feb―12 |
The Effect of Point Mutations on Structure and Dynamics of SARS-CoV-2 Main Protease Mutants |
Elizabeth M. Diessner, Zixiao Zong, Thomas J. Cross, Gemma R. Takahashi, Marquise G. Crosby, Vesta Farahmad, Shannon Zhuang, Carter T. Butts, Rachel W. Martin |
| 211 |
[GO] |
2021―Feb―12 |
Force-Dependent Stimulation of RNA Unwinding by SARS-CoV-2 NSP13 Helicase |
Keith J. Mickolajczyk, Patrick M. Shelton, Michael Grasso, Xiaocong Cao, Sara E. Warrington, Amol Aher, Shixin Liu, Tarun M. Kapoor |
| 212 |
[GO] |
2021―Feb―12 |
DNA Folding by the SARS-CoV-2 Nucleocapsid Protein |
Youna N. Choi, Ryan B. McMillan, Ashley R. Carter |
| 213 |
[GO] |
2021―Feb―12 |
Investigating SARS-CoV-2 Orf7B Homodimerization by Molecular Dynamics Simulations |
Min-Kang Hsieh, Jeffery B. Klauda |
| 214 |
[GO] |
2021―Feb―12 |
Dynamics and Binding Strength of the Spike Protein of Sars-Cov-2 Probed by High-Speed Atomic Force Microscopy |
Fidan Sumbul, Claire Valotteau, Ignacio Fernandez, Analisa Meola, Eduard Baquero, Dorota Kostrz, Charlie Gosse, Terence R. Strick, Felix Rey, Felix Rico |
| 215 |
[GO] |
2021―Feb―12 |
Automated Computational Technique to Improve the Quality of SARS-CoV-2 Proteins |
Joseph P. Farrell, Esmael J. Haddadian |
| 216 |
[GO] |
2021―Feb―12 |
Using Tactics to Find Druggable Pockets in SARS-CoV-2 Proteins |
Daniel J. Evans, Remy A. Yovanno, Sanim Rahman, Afif Bandak, Albert Y. Lau |
| 217 |
[GO] |
2021―Feb―12 |
Prediction and Analysis of Multiple Sites and Inhibitors of SARS-CoV-2 Proteins |
Suhasini M. Iyengar, Kelton Barnsley, Hoang Yen Vu, Ryan Dilworth, Jana Sefcikova, Penny Beuning, Mary Jo Ondrechen |
| 218 |
[GO] |
2021―Feb―12 |
Characterizing Binding Kinetics and Thermodynamics of Computer-Designed Nanobodies Targeting SARS-CoV-2 RBD |
Matheus Ferraz, Roberto Lins |
| 219 |
[GO] |
2021―Feb―12 |
Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2 |
Kien Nguyen, Srirupa Chakraborty, Rachael A. Mansbach, Pedro D. Manrique, Bette Korber, Sandrasegaram Gnanakaran |
| 220 |
[GO] |
2021―Feb―12 |
The Effect of Mutations on Binding Interactions Between the SARS-CoV-2 Receptor Binding Domain and Neutralizing Antibodies |
Jonathan E. Barnes, Peik K. Lund-Andersen, Jagdish S. Patel, F. Marty Ytreberg |
| 221 |
[GO] |
2021―Feb―12 |
Modeling the Structure of the Frameshift-Stimulatory Pseudoknot in SARS-CoV-2 Reveals Multiple Possible Conformers |
Sara Ibrahim Omar, Meng Zhao, Rohith Vedhthaanth Sekar, Sahar Arbabimoghadam, Jack A. Tuszynski, Michael T. Woodside |
| 222 |
[GO] |
2021―Feb―12 |
Energetics of Opening for the Glycosylated and Unglycosylated Forms of the SARS-CoV-2 S-Protein Trimer |
Yui Tik Pang, Atanu Acharya, Diane L. Lynch, James C. Gumbart |
| 223 |
[GO] |
2021―Feb―12 |
Enhanced Sampling of the SARS-CoV-2 s2m Element |
Adam H. Kensinger, Kendy A. Pellegrene, Joshua Imperatore, Matthew N. Srnec, Mihaela-Rita Mihailescu, Jeffrey D. Evanseck |
| 224 |
[GO] |
2021―Feb―12 |
Condensed Liquid Phase 3D Structure of SARS-CoV-2 s2m Guided by NMR Spectroscopy |
Kendy A. Pellegrene, Joshua A. Imperatore, Caylee L. Cunningham, Adam H. Kensinger, Petru Mihailescu, Matthew N. Srnec, Mihaela-Rita Mihailescu, Jeffrey D. Evanseck |
| 225 |
[GO] |
2021―Feb―12 |
SARS-CoV-2 Simulations go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome |
Maxwell I. Zimmerman, Gregory Bowman |
| 226 |
[GO] |
2021―Feb―12 |
Essential Dynamics that Drive Sars-Cov-2 Spike Conformational Changes |
Srirupa Chakraborty, Rachael A. Mansbach, Kien Nguyen, Pedro D. Manrique, Sandrasegaram Gnanakaran |
| 227 |
[GO] |
2021―Feb―12 |
Identifying Hotspots in Binding of SARS-CoV-2 Spike Glycoprotein and Human ACE2 |
Jenny Mendis, Ekrem Kaya, Tugba G. Kucukkal |
| 228 |
[GO] |
2021―Feb―12 |
Inhibition of SARS-CoV-2 Spike Protein Function by Amphiphilic Block Copolymers |
Michelle X. Ling, Michelle Nguyen, Kyle McCollum, Raphael C. Lee |
| 229 |
[GO] |
2021―Feb―12 |
Refinement of the Transmembrane Domain in Constructing the Membrane-Embedded SARS-COV-2 Spike Protein Model |
Tianle Chen, Karan Kapoor, Emad Tajkhorshid |
| 230 |
[GO] |
2021―Feb―12 |
The Influence of Glycosylation on the Interaction of the Sars-Cov-2 Spike Protein Receptor Binding Domain with Therapeutic Candidates. |
Bradley Harris, Yihan Huang, Giovanni Lara, Shiaki Minami, Matthew Kenaston, Seongwon Jung, Yongao Xiong, Karen McDonald, Somen Nandi, Priya Shah, Roland Faller |
| 231 |
[GO] |
2021―Feb―12 |
The Extended Intermediate of the SARS-CoV-2 Spike Protein uses Extreme Reach and Flexibility to Capture Host Cell Membranes |
Rui Su, Jin Zeng, Sathish Thiyagarajan, Ben O'Shaughnessy |
| 232 |
[GO] |
2021―Feb―12 |
Mapping Binding Interfaces and Allosteric Changes in the SARS-Cov-2 Spike Protein using Hydrogen/Deuterium Exchange Mass Spectrometry |
Shawn M. Costello, Helen T. Hobbs, Sophie R. Shoemaker, Abigail E. Powell, Shion A. Lim, James A. Wells, Peter S. Kim, John E. Pak, Susan Marqusee |
| 233 |
[GO] |
2021―Feb―12 |
The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State |
Rachael A. Mansbach, Srirupa Chakraborty, Kien Nguyen, David C. Montefiori, Bette Korber, Gnana Gnanakaran |
| 234 |
[GO] |
2021―Feb―12 |
Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles |
Maolin Lu, Pradeep D. Uchil, Wenwei Li, Daniel S. Terry, Jason Gorman, Baoshang Zhang, Tongqing Zhou, Shilei Ding, Lihong Liu, David D. Ho, John R. Mascola, Andrés Finzi, Peter Kwong, Scott C. Blanchard, Walther Mothes |
| 235 |
[GO] |
2021―Feb―12 |
Predicting the Ability of SARS-CoV-2 to Utilize the ACE2 Receptor for Cell Entry in North American Rodents |
Peik K. Lund-Andersen, Jeremy R. Ellis, James T. Van Leuven, Jagdish Patel |
| 236 |
[GO] |
2021―Feb―12 |
Understanding Activation and Inhibition of SARS-CoV-2 Viral Entry with Single-Virus Microscopy |
Anjali Sengar, Giorgio Morbioli, Peter Kasson |
| 237 |
[GO] |
2021―Feb―12 |
Topography, Spike Dynamics and Nanomechanics of Individual Native SARS-CoV-2 Virions |
Balint Kiss, Zoltán Kis, Bernadett Pályi, Miklós S. Kellermayer |
| 238 |
[GO] |
2021―Feb―12 |
Adaptive Evolution of SARS-CoV-2: A Perspective from Dynamics |
Ismail C. Kazan, S. Banu Ozkan |
| 239 |
[GO] |
2021―Feb―12 |
Conserved Elements in the 3'-UTR of SARS-CoV-2: Involvement in Genomic Dimerization and Interactions with Cellular Micrornas |
Joshua A. Imperatore, Caylee L. Cunningham, Caleb J. Frye, Kendy A. Pellegrene, Jeffrey D. Evanseck, Mihaela-Rita Mihailescu |
| 240 |
[GO] |
2021―Feb―12 |
Mechanism and Pathways of Inhibitor Binding to the Human ACE2 Receptor for SARS-CoV1/2 |
Apurba Bhattarai, Shristi Pawnikar, Yinglong Miao |
| 241 |
[GO] |
2021―Feb―12 |
Factors that Affect the Binding of the N-Terminal Helix of Human ACE2 to Spike Protein of SARS-CoV2 |
Anirban Das, Vicky Vishvakarma, Ankur Gupta, Simli Dey, Arpan Dey, U. Sandra, Ullas Kolthur, Mitradip Das, Krishna K. Vishwakarma, Ravindra Venkatramani, Sudipta Maiti |
| 242 |
[GO] |
2021―Feb―12 |
Elucidating the Mechanism of Membrane Destabilization by the Preferred Modes of Insertion of the Sars-Cov2 Fusion Peptide |
George Khelashvili, Harel Weinstein |
| 243 |
[GO] |
2021―Feb―12 |
Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membranes |
Defne Gorgun, Muyun Lihan, Karan Kapoor, Emad Tajkhorshid |
| 244 |
[GO] |
2021―Feb―12 |
Hepatitis C Virus Protease Inhibitors Suppress Virus Replication and Act Synergistically with the SARS-CoV2 Polymerase Inhibitor Remdesivir |
Khushboo Bafna, Kris White, Balasubramanian Harish, Catherine A. Royer, Adolfo Garcia-Sastre, Robert M. Krug, Gaetano T. Montelione |
| 245 |
[GO] |
2021―Feb―03 |
Bow to the Enemy: How Flexibility of Host Protein Receptors Can Favor SARS-CoV-2 |
Stefano A. Serapian, Giorgio Colombo |
| 246 |
[GO] |
2021―Feb―03 |
Graph, Pseudoknot, and SARS-Cov-2 Genomic RNA - a Biophysical Synthesis |
Shi-Jie Chen |
| 247 |
[GO] |
2021―Jan―26 |
A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion |
John E. Straub |
| 248 |
[GO] |
2021―Jan―21 |
Elucidation of Interactions Regulating Conformational Stability and Dynamics of SARS-CoV-2 S-Protein |
Takaharu Mori, Jaewoon Jung, Chigusa Kobayashi, Hisham M. Dokainish, Suyong Re, Yuji Sugita |
| 249 |
[GO] |
2021―Jan―17 |
Improving SARS-CoV-2 Structures: Peer Review by Early Coordinate Release |
Tristan I. Croll, Christopher J. Williams, Vincent B. Chen, David C. Richardson, Jane S. Richardson |
| 250 |
[GO] |
2020―Dec―25 |
The molecular mechanism of domain-swapping of the C-terminal domain of the SARS coronavirus main protease |
Vishram L. Terse, Shachi Gosavi |
| 251 |
[GO] |
2020―Dec―17 |
Force-dependent stimulation of RNA unwinding by SARS-CoV-2 nsp13 helicase |
Keith J. Mickolajczyk, Patrick M.M. Shelton, Michael Grasso, Xiaocong Cao, Sara E. Warrington, Amol Aher, Shixin Liu, Tarun M. Kapoor |
| 252 |
[GO] |
2020―Nov―28 |
Thermal Inactivation Scaling Applied for SARS-CoV-2 |
Shahar Seifer, Michael Elbaum |
| 253 |
[GO] |
2020―Nov―28 |
A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion |
Alvin Yu, Alexander J. Pak, Peng He, Viviana Monje-Galvan, Lorenzo Casalino, Zied Gaieb, Abigail C. Dommer, Rommie E. Amaro, Gregory A. Voth |
| 254 |
[GO] |
2020―Nov―13 |
The flexibility of ACE2 in the context of SARS-CoV-2 infection |
Emilia P. Barros, Lorenzo Casalino, Zied Gaieb, Abigail C. Dommer, Yuzhang Wang, Lucy Fallon, Lauren Raguette, Kellon Belfon, Carlos Simmerling, Rommie E. Amaro |
| 255 |
[GO] |
2020―Oct―21 |
Structure-Altering Mutations of the SARS-CoV-2 Frame Shifting RNA Element |
Tamar Schlick, Qiyao Zhu, Swati Jain, Shuting Yan |
| 256 |
[GO] |
2020―Aug―08 |
Reflections on the Pandemic |
H. Jane Dyson |
