|
original article |
Date |
Title |
Authors All 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, et al. (+7) 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, et al. (+3) 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, et al. (+2) 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, et al. (+3) 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, et al. (+6) 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, et al. (+2) 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, et al. (+3) 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, et al. (+2) 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, et al. (+2) 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, et al. (+6) 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, et al. (+3) 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, et al. (+4) 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, et al. (+2) 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, et al. (+3) 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, et al. (+6) 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, et al. (+3) 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 |