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63 Results       Page 1

 [1] 
American Chemical Society: The Journal of Physical Chemistry Letters
  original article Date Title Authors   Max. 6 Authors
1 [GO] 2024―Jan―19 Structural Insights into SARS-CoV-2 Nonstructural Protein 1 Interaction with Human Cyclophilin and FKBP1 to Regulate Interferon Production Naveen Vankadari, Debnath Ghosal
2 [GO] 2024―Jan―11 Novel Omicron Variants Enhance Anchored Recognition of TMEM106B: A New Pathway for SARS-CoV-2 Cellular Invasion Xiaoyu Zhao, Feng Gao
3 [GO] 2023―Nov―13 Dynamic Counterion Condensation Model Decodes Functional Dynamics of RNA Pseudoknot in SARS-CoV-2: Control of Ion-Mediated Pierced Lasso Topology Avijit Mainan, Susmita Roy
4 [GO] 2023―Nov―09 Unmasking an Allosteric Binding Site of the Papain-like Protease in SARS-CoV-2: Molecular Dynamics Simulations of Corticosteroids Saroj Kumar Panda, Parth Sarthi Sen Gupta, Shaswata Karmakar, Satyaranjan Biswal, Nimai Charan Mahanandia, Malay Kumar Rana
5 [GO] 2023―Nov―03 SARS-CoV-2 RNA-Dependent RNA Polymerase Follows Asynchronous Translocation Pathway for Viral Transcription and Replication Xiaowei Wang, Tiantian Xu, Yuan Yao, Peter Pak-Hang Cheung, Xin Gao, Lu Zhang
6 [GO] 2023―Oct―18 Data Driven Computational Design and Experimental Validation of Drugs for Accelerated Mitigation of Pandemic-like Scenarios Samrendra K. Singh, Kelsie King, Cole Gannett, Christina Chuong, Soumil Y. Joshi, Charles Plate, Parisa Farzeen, Emily M. Webb, Lakshmi Kumar Kunche, James Weger-Lucarelli, Andrew N. Lowell, Anne M. Brown, Sanket A. Deshmukh
7 [GO] 2023―Oct―02 Dissecting the Molecular Basis of Host Leucine-Rich Repeat Containing 15 Mediated Interaction with Receptor Binding Domain of SARS-CoV-2 Spike Protein: A Computational Approach Sarbani Mishra, Mansi Sharma, Mahendra Kumar Singh, Sanghamitra Pati, Budheswar Dehury
8 [GO] 2023―Sep―14 Nanoscopic Elucidation of Spontaneous Self-Assembly of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Open Reading Frame 6 (ORF6) Protein Goro Nishide, Keesiang Lim, Maiki Tamura, Akiko Kobayashi, Qingci Zhao, Masaharu Hazawa, Toshio Ando, Noritaka Nishida, Richard W. Wong
9 [GO] 2023―Jun―23 Modeling the Interaction of Coronavirus Membrane Phospholipids with Photocatalitically Active Titanium Dioxide Iván Soriano-Díaz, Eros Radicchi, Beatrice Bizzarri, Olivia Bizzarri, Edoardo Mosconi, Muhammad Waqar Ashraf, Filippo De Angelis, Francesca Nunzi
10 [GO] 2023―Apr―06 Quantum Chemical Interaction Analysis between SARS-CoV-2 Main Protease and Ensitrelvir Compared with Its Initial Screening Hit Chiduru Watanabe, Shigenori Tanaka, Yoshio Okiyama, Hitomi Yuki, Tatsuya Ohyama, Kikuko Kamisaka, Daisuke Takaya, Kaori Fukuzawa, Teruki Honma
11 [GO] 2023―Mar―27 How SARS-CoV-2 Alters the Regulation of Gene Expression in Infected Cells Emmanuelle Bignon, Stéphanie Grandemange, Elise Dumont, Antonio Monari
12 [GO] 2022―Dec―27 Rapid Detection of SARS-CoV-2 Spike RBD Protein in Body Fluid: Based on Special Calcium Ion-Mediated Gold Nanoparticles Modified by Bromide Ions Fenghai Zhang, Xiaotong Wang, Ting Zhang, Zhe Zhang, Xin Gao, Yang Li
13 [GO] 2022―Nov―10 Moderate Binding between Two SARS-CoV-2 Protein Segments and α-Synuclein Alters Its Toxic Oligomerization Propensity Differently Vince St. Dollente Mesias, Hongni Zhu, Xiao Tang, Xin Dai, Wei Liu, Yusong Guo, Jinqing Huang
14 [GO] 2022―Sep―20 Molecular Mechanism of the Non-Covalent Orally Targeted SARS-CoV-2 Mpro Inhibitor S-217622 and Computational Assessment of Its Effectiveness against Mainstream Variants Danyang Xiong, Xiaoyu Zhao, Song Luo, John Z. H. Zhang, Lili Duan
15 [GO] 2022―Aug―31 S2 Subunit of SARS-CoV-2 Spike Protein Induces Domain Fusion in Natural Pulmonary Surfactant Monolayers Xiaojie Xu, Guangle Li, Bingbing Sun, Yi Y. Zuo
16 [GO] 2022―Aug―05 Identification of Potential ACE2-Derived Peptide Mimetics in SARS-CoV-2 Omicron Variant Therapeutics using Computational Approaches Stanly Paul, Swathi Nadendla, M Elizabeth Sobhia
17 [GO] 2022―Jul―30 Unveiling the “Template-Dependent” Inhibition on the Viral Transcription of SARS-CoV-2 Xueying Luo, Xiaowei Wang, Yuan Yao, Xin Gao, Lu Zhang
18 [GO] 2022―Jun―27 Immune Escape Mechanisms of SARS-CoV-2 Delta and Omicron Variants against Two Monoclonal Antibodies That Received Emergency Use Authorization Danyang Xiong, Xiaoyu Zhao, Song Luo, Yalong Cong, John Z. H. Zhang, Lili Duan
19 [GO] 2022―Jun―21 Primer for Designing Main Protease (Mpro) Inhibitors of SARS-CoV-2 Abhishek Thakur, Gaurav Sharma, Vishnu Nayak Badavath, Venkatesan Jayaprakash, Kenneth M. Merz, Galia Blum, Orlando Acevedo
20 [GO] 2022―Jun―08 Structure of Human TMPRSS2 in Complex with SARS-CoV-2 Spike Glycoprotein and Implications for Potential Therapeutics Naveen Vankadari, Vijayasarathy Ketavarapu, Sasikala Mitnala, Ravikanth Vishnubotla, Duvvur Nageshwar Reddy, Debnath Ghosal
21 [GO] 2022―May―20 Correction to “Elucidation of SARS-Cov-2 Budding Mechanisms through Molecular Dynamics Simulations of M and E Protein Complexes” Logan Thrasher Collins, Tamer Elkholy, Shafat Mubin, David Hill, Ricky Williams, Kayode Ezike, Ankush Singhal
22 [GO] 2022―May―20 Hijacking of Cellular Functions by Severe Acute Respiratory Syndrome Coronavirus-2. Permeabilization and Polarization of the Host Lipid Membrane by Viroporins Emmanuelle Bignon, Marco Marazzi, Antonio Monari
23 [GO] 2022―May―03 2′- and 3′-Ribose Modifications of Nucleotide Analogues Establish the Structural Basis to Inhibit the Viral Replication of SARS-CoV-2 Yongfang Li, Dong Zhang, Xin Gao, Xiaowei Wang, Lu Zhang
24 [GO] 2021―Dec―20 Elucidation of SARS-Cov-2 Budding Mechanisms through Molecular Dynamics Simulations of M and E Protein Complexes Logan Thrasher Collins, Tamer Elkholy, Shafat Mubin, David Hill, Ricky Williams, Kayode Ezike, Ankush Singhal
25 [GO] 2021―Dec―07 Mechanisms of SARS-CoV-2 Evolution Revealing Vaccine-Resistant Mutations in Europe and America Rui Wang, Jiahui Chen, Guo-Wei Wei
26 [GO] 2021―Dec―01 Molecular Basis of SARS-CoV-2 Nsp1-Induced Immune Translational Shutdown as Revealed by All-Atom Simulations Jure Borišek, Angelo Spinello, Alessandra Magistrato
27 [GO] 2021―Nov―12 Interaction Analysis on the SARS-CoV-2 Spike Protein Receptor Binding Domain Using Visualization of the Interfacial Electrostatic Complementarity Takeshi Ishikawa, Hiroki Ozono, Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Yuji Mochizuki
28 [GO] 2021―Nov―11 Role of Ionizable Lipids in SARS-CoV-2 Vaccines As Revealed by Molecular Dynamics Simulations: From Membrane Structure to Interaction with mRNA Fragments Markéta Paloncýová, Petra Čechová, Martin Šrejber, Petra Kührová, Michal Otyepka
29 [GO] 2021―Oct―17 Structure and Dynamics of RNA Guanine Quadruplexes in SARS-CoV-2 Genome. Original Strategies against Emerging Viruses Tom Miclot, Cécilia Hognon, Emmanuelle Bignon, Alessio Terenzi, Marco Marazzi, Giampaolo Barone, Antonio Monari
30 [GO] 2021―Jul―01 Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface Dina El Ahdab, Louis Lagardère, Théo Jaffrelot Inizan, Fréderic Célerse, Chengwen Liu, Olivier Adjoua, Luc-Henri Jolly, Nohad Gresh, Zeina Hobaika, Pengyu Ren, Richard G. Maroun, Jean-Philip Piquemal
31 [GO] 2021―Jul―01 Regulation Mechanism for the Binding between the SARS-CoV-2 Spike Protein and Host Angiotensin-Converting Enzyme II Haiyi Chen, Yu Kang, Mojie Duan, Tingjun Hou
32 [GO] 2021―Jun―23 Allosteric Cross-Talk among Spike’s Receptor-Binding Domain Mutations of the SARS-CoV-2 South African Variant Triggers an Effective Hijacking of Human Cell Receptor Angelo Spinello, Andrea Saltalamacchia, Jure Borišek, Alessandra Magistrato
33 [GO] 2021―Jun―10 Conformational Dynamics in the Interaction of SARS-CoV-2 Papain-like Protease with Human Interferon-Stimulated Gene 15 Protein Wellington C. Leite, Kevin L. Weiss, Gwyndalyn Phillips, Qiu Zhang, Shuo Qian, Susan E. Tsutakawa, Leighton Coates, Hugh O’Neill
34 [GO] 2021―Jun―04 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, Chris Chipot, James C. Gumbart
35 [GO] 2021―Apr―26 Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design Laura Zanetti-Polzi, Micholas Dean Smith, Chris Chipot, James C. Gumbart, Diane L. Lynch, Anna Pavlova, Jeremy C. Smith, Isabella Daidone
36 [GO] 2021―Apr―23 Intermolecular Interaction Analyses on SARS-CoV-2 Spike Protein Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/Peptide Using Fragment Molecular Orbital Calculation Kazuki Watanabe, Chiduru Watanabe, Teruki Honma, Yu-Shi Tian, Yusuke Kawashima, Norihito Kawashita, Tatsuya Takagi, Kaori Fukuzawa
37 [GO] 2021―Mar―10 Theoretical Analysis Reveals the Cost and Benefit of Proofreading in Coronavirus Genome Replication Joel D. Mallory, Xian F. Mallory, Anatoly B. Kolomeisky, Oleg A. Igoshin
38 [GO] 2021―Feb―13 Kobophenol A Inhibits Binding of Host ACE2 Receptor with Spike RBD Domain of SARS-CoV-2, a Lead Compound for Blocking COVID-19 Suresh Gangadevi, Vishnu Nayak Badavath, Abhishek Thakur, Na Yin, Steven De Jonghe, Orlando Acevedo, Dirk Jochmans, Pieter Leyssen, Ke Wang, Johan Neyts, Tao Yujie, Galia Blum
39 [GO] 2021―Feb―02 Retrained Generic Antibodies Can Recognize SARS-CoV-2 Yanxiao Han, Katherine D. McReynolds, Petr Král
40 [GO] 2021―Jan―29 On Drug-Membrane Permeability of Antivirals for SARS-CoV-2 Changjiang Liu, Paolo Elvati, Angela Violi
41 [GO] 2020―Dec―12 Candidate Binding Sites for Allosteric Inhibition of the SARS-CoV-2 Main Protease from the Analysis of Large-Scale Molecular Dynamics Simulations Matteo Carli, Giulia Sormani, Alex Rodriguez, Alessandro Laio
42 [GO] 2020―Dec―05 Computational Insights into the Conformational Accessibility and Binding Strength of SARS-CoV-2 Spike Protein to Human Angiotensin-Converting Enzyme 2 Cheng Peng, Zhengdan Zhu, Yulong Shi, Xiaoyu Wang, Kaijie Mu, Yanqing Yang, Xinben Zhang, Zhijian Xu, Weiliang Zhu
43 [GO] 2020―Dec―03 Molecular Dynamics Reveals Complex Compensatory Effects of Ionic Strength on the Severe Acute Respiratory Syndrome Coronavirus 2 Spike/Human Angiotensin-Converting Enzyme 2 Interaction Anacleto Silva de Souza, Jose David Rivera, Vitor Medeiros Almeida, Pingju Ge, Robson Francisco de Souza, Chuck Shaker Farah, Henning Ulrich, Sandro Roberto Marana, Roberto Kopke Salinas, Cristiane Rodrigues Guzzo
44 [GO] 2020―Nov―23 Theoretical Design of Functionalized Gold Nanoparticles as Antiviral Agents against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Aliyeh Mehranfar, Mohammad Izadyar
45 [GO] 2020―Nov―12 Decoding Asymptomatic COVID-19 Infection and Transmission Rui Wang, Jiahui Chen, Yuta Hozumi, Changchuan Yin, Guo-Wei Wei
46 [GO] 2020―Nov―11 Epitope-Based Potential Vaccine Candidate for Humoral and Cell-Mediated Immunity to Combat Severe Acute Respiratory Syndrome Coronavirus 2 Pandemic Bratin Kumar Das, Debashree Chakraborty
47 [GO] 2020―Nov―05 In Silico Antibody Mutagenesis for Optimizing Its Binding to Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2 Binquan Luan, Tien Huynh
48 [GO] 2020―Nov―02 Structure of the SARS-CoV-2 Nsp1/5′-Untranslated Region Complex and Implications for Potential Therapeutic Targets, a Vaccine, and Virulence Naveen Vankadari, Nandhini Nisha Jeyasankar, Wilma Jerom Lopes
49 [GO] 2020―Oct―26 COSMO-RS-Based Descriptors for the Machine Learning-Enabled Screening of Nucleotide Analogue Drugs against SARS-CoV-2 Sergey Gusarov, Stanislav R. Stoyanov
50 [GO] 2020―Oct―21 Thermodynamics of the Interaction between the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus-2 and the Receptor of Human Angiotensin-Converting Enzyme 2. Effects of Possible Ligands Cristina García-Iriepa, Cécilia Hognon, Antonio Francés-Monerris, Isabel Iriepa, Tom Miclot, Giampaolo Barone, Antonio Monari, Marco Marazzi
51 [GO] 2020―Oct―14 Discovery of COVID-19 Inhibitors Targeting the SARS-CoV-2 Nsp13 Helicase Mark Andrew White, Wei Lin, Xiaodong Cheng
52 [GO] 2020―Sep―04 The Answer Lies in the Energy: How Simple Atomistic Molecular Dynamics Simulations may Hold the Key to Epitope Prediction on the Fully Glycosylated SARS-CoV-2 Spike Protein Stefano Artin Serapian, Filippo Marchetti, Alice Triveri, Giulia Morra, Massimiliano Meli, Elisabetta Moroni, Giuseppe A. Sautto, Andrea Rasola, Giorgio Colombo
53 [GO] 2020―Aug―25 Alkamides and Piperamides as Potential Antivirals Against the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Juan Manuel Gutierrez-Villagomez, Tonatiu Campos-García, Jorge Molina Torres, Mercedes G. López, Juan Vázquez-Martínez
54 [GO] 2020―Aug―05 Screening of Therapeutic Agents for COVID-19 Using Machine Learning and Ensemble Docking Studies Rohit Batra, Henry Chan, Ganesh Kamath, Rampi Ramprasad, Mathew J. Cherukara, Subramanian K.R.S. Sankaranarayanan
55 [GO] 2020―Aug―03 Dynamic Asymmetry Exposes 2019-nCoV Prefusion Spike Susmita Roy, Akhilesh Jaiswar, Raju Sarkar
56 [GO] 2020―Jul―28 Repurposing Low-Molecular-Weight Drugs Against the Main Protease of Severe Acute Respiratory Syndrome Coronavirus 2 Jia Gao, Liang Zhang, Xiaodan Liu, Fudong Li, Rongsheng Ma, Zhongliang Zhu, Jiahai Zhang, Jihui Wu, Yunyu Shi, Yueyin Pan, Yushu Ge, Ke Ruan
57 [GO] 2020―Jul―28 Structure of Furin Protease Binding to SARS-CoV-2 Spike Glycoprotein and Implications for Potential Targets and Virulence Naveen Vankadari
58 [GO] 2020―Jun―16 Repositioning of 8565 Existing Drugs for COVID-19 Kaifu Gao, Duc D. Nguyen, Jiahui Chen, Rui Wang, Guowei Wei
59 [GO] 2020―Jun―15 Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses Cecilia Hognon, Tom Miclot, Cristina Garcia-Iriepa, Antonio Francés-Monerris, Stephanie Grandemange, Alessio Terenzi, Marco Marazzi, Giampaolo Barone, Antonio Monari
60 [GO] 2020―Jun―01 Comparing the Binding Interactions in the Receptor Binding Domains of SARS-CoV-2 and SARS-CoV Muhamed Amin, Mariam K. Sorour, Amal Kasry
61 [GO] 2020―May―28 Is the Rigidity of SARS-CoV-2 Spike Receptor-Binding Motif the Hallmark for Its Enhanced Infectivity? Insights from All-Atoms Simulations Angelo Spinello, Andrea Saltalamacchia, Alessandra Magistrato
62 [GO] 2020―May―14 In Silico Exploration of Molecular Mechanism of Clinically Oriented Drugs for Possibly Inhibiting SARS-CoV-2's Main Protease Tien Huynh, Haoran Wang, Binquan Luan
63 [GO] 2020―May―11 Novel Coronavirus Polymerase and Nucleotidyl-transferase Structures: Potential to Target New Outbreaks Wenfa Zhang, Preyesh Stephen, Jean-François Thériault, Ruixuan Wang, Sheng-Xiang Lin
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63 Results       Page 1



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