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original article |
Date |
Title |
Authors Max. 6 Authors |
| 1 |
[GO] |
2026―Jul―03 |
Predicting Nirmatrelvir Resistance in SARS-CoV-2 M
pro
Mutants with an Integrated Computational Framework |
Fanyu Zhao, Wei Xia, Yuzhi Xu, Xue Wu, Shiyu Hu, John Z. H. Zhang |
| 2 |
[GO] |
2026―May―18 |
Quantitative Analysis of Protein-Receptor Binding Using Solid-State Nanopores: Accurate Measurement of Dissociation Constants for KREMEN1 and ASGR1 with SARS-CoV-2 Spike RBD Protein |
Matthew O’Donohue, Navod Thyashan, Min Jun Kim |
| 3 |
[GO] |
2026―Apr―30 |
Mass Photometry Reveals Distinct ACE2 Binding Stoichiometries across SARS-CoV-2 Omicron Subvariants |
Wei-Cheng Hsiao, Tsung-Sheng Chiang, Yu-Xi Tsai, Min-Feng Hsu, Shang-Te Danny Hsu |
| 4 |
[GO] |
2026―Mar―12 |
Pentameric Architecture of the SARS-CoV-2 Envelope Protein Revealed by SEC-MALS, Cryo-EM, and Molecular Dynamics |
Zi-Wen Weng, Danny Farhat, Jyh-Yeuan Lee, Shang-Te Danny Hsu |
| 5 |
[GO] |
2026―Feb―02 |
Conformational Heterogeneity and Redox Switching of the Cysteine Residues in SARS-CoV-2 Main Protease: A Raman Molecular Fingerprint |
Banadipa Nanda, Anupam Maity, Rajendra Prasad Nandi, Sandip Dolui, Rajdip Misra, Uttam Pal, Nakul C. Maiti |
| 6 |
[GO] |
2025―Dec―20 |
Integrating Network Pharmacology to Investigate the Mechanism of Ginsenoside Compound K Against Coronavirus |
Zhihang Qu, Yi Wang, Hongshan Yu, Siyu Xu |
| 7 |
[GO] |
2025―Nov―10 |
Design of Carbon Nanotube Inhibitors for Main Proteinase of SARS-CoV-2: A Combined Deep Learning and Molecular Dynamics Simulation Study |
Yunju Zhang, Zechen Wang, Yanmei Yang, Yuanyuan Qu, Yong-Qiang Li, Qingmeng Zhang, Mingwen Zhao, Yuguang Mu, Weifeng Li |
| 8 |
[GO] |
2025―Aug―08 |
Conformational Sampling during the Reaction of the SARS-CoV-2 Methyltransferase nsp16 |
Yuanxin Cao, James D. Green, Linus O. Johannissen, Sam Hay |
| 9 |
[GO] |
2025―Aug―04 |
Advanced Computational Approaches to Evaluate the Potential of New-Generation Adamantane-Based Drugs as Viroporin Inhibitors: A Case Study on SARS-CoV-2 |
Sarina Yousefbeigi, Farah Marsusi |
| 10 |
[GO] |
2025―May―19 |
Computational and Experimental Study of the Conformational Variation of the Catalytic Residue His41 of the SARS-CoV-2 Main Protease |
Jiao Zhou, Xiang Liu, Yan Xu, Juan Wang, Tingli Qian, Xiaohong Sang, Md Nazmul Hasan, Arieh Warshel, Jing An, Arjun Saha, Ziwei Huang |
| 11 |
[GO] |
2025―Jan―31 |
In Silico Discovery of SARS-CoV-2 Main Protease Inhibitors Using Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations |
Takeshi Ishikawa, Kenji Matsumoto, Toshiyuki Hamada, Hinako Koze, Masanori Baba, Mika Okamoto, Masayuki Sudoh |
| 12 |
[GO] |
2024―Dec―18 |
Sequence of the SARS-CoV-2 Spike Transmembrane Domain Encodes Conformational Dynamics |
Sahil Lall, Padmanabhan Balaram, M. K. Mathew, Shachi Gosavi |
| 13 |
[GO] |
2024―Dec―03 |
Identification of RdRp-NiRAN/JAK1 Dual-Target Drugs for COVID-19 Treatment |
Huixuan Zhao, Xiaoyu Chang, Lei Sun, Ertong Li, Depeng Zhang, Wentao Qi, Jijie Chai, Xueping Hu, Weiqiao Deng |
| 14 |
[GO] |
2024―Jul―16 |
Neuropilin-1 Protein May Serve as a Receptor for SARS-CoV-2 Infection: Evidence from Molecular Dynamics Simulations |
Hoang Linh Nguyen, Ho Khac Hieu, Thai Quoc Nguyen, Nguyen Thi Ai Nhung, Mai Suan Li |
| 15 |
[GO] |
2024―Jul―15 |
Binding of SARS-CoV-2 Nonstructural Protein 1 to 40S Ribosome Inhibits mRNA Translation |
Hung Nguyen, Hoang Linh Nguyen, Mai Suan Li |
| 16 |
[GO] |
2024―May―02 |
AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between Convergent Mutational Hotspots that Control ACE2 Affinity |
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady Verkhivker |
| 17 |
[GO] |
2024―Apr―24 |
A Rationally Designed Synthetic Antiviral Peptide Binder Targeting the Receptor-Binding Domain of SARS-CoV-2 |
Lalita Mohan Behera, Pulkit Kr. Gupta, Manaswini Ghosh, Sucharita Shadangi, Soumendra Rana |
| 18 |
[GO] |
2024―Apr―02 |
SARS-CoV-2 Omicron Subvariants Do Not Differ Much in Binding Affinity to Human ACE2: A Molecular Dynamics Study |
Hoang Linh Nguyen, Thai Quoc Nguyen, Mai Suan Li |
| 19 |
[GO] |
2024―Mar―11 |
Bis(Monoacylglycero)Phosphate Promotes Membrane Fusion Facilitated by the SARS-CoV-2 Fusion Domain |
Daniel Birtles, Wafa Abbas, Jinwoo Lee |
| 20 |
[GO] |
2024―Mar―04 |
Prediction of Binding Pose and Affinity of Nelfinavir, a SARS-CoV-2 Main Protease Repositioned Drug, by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations |
Yuma Handa, Koji Okuwaki, Yusuke Kawashima, Ryo Hatada, Yuji Mochizuki, Yuto Komeiji, Shigenori Tanaka, Takayuki Furuishi, Etsuo Yonemochi, Teruki Honma, Kaori Fukuzawa |
| 21 |
[GO] |
2024―Jan―08 |
Two Receptor Binding Strategy of SARS-CoV-2 Is Mediated by Both the N-Terminal and Receptor-Binding Spike Domain |
Michele Monti, Edoardo Milanetti, Myrthe T. Frans, Mattia Miotto, Lorenzo Di Rienzo, Maksim V. Baranov, Giorgio Gosti, Arun Kumar Somavarapu, Madhu Nagaraj, Thaddeus W. Golbek, Emiel Rossing, Sam J. Moons, Thomas J. Boltje, Geert van den Bogaart, Tobias Weidner, Daniel E. Otzen, Gian Gaetano Tartaglia, Giancarlo Ruocco, Steven J. Roeters |
| 22 |
[GO] |
2024―Jan―04 |
Role of ATP Hydrolysis and Product Release in the Translocation Mechanism of SARS-CoV-2 NSP13 |
Monsurat M. Lawal, Priti Roy, Martin McCullagh |
| 23 |
[GO] |
2023―Dec―26 |
Multiscale Molecular Dynamics Simulations of the Homodimer Accessory Protein ORF7b of SARS-CoV-2 |
Min-Kang Hsieh, Jeffery B. Klauda |
| 24 |
[GO] |
2023―Oct―10 |
From De Novo Design to Redesign: Harnessing Computational Protein Design for Understanding SARS-CoV-2 Molecular Mechanisms and Developing Therapeutics |
Aditya K. Padhi, Parismita Kalita, Shweata Maurya, Krishna Mohan Poluri, Timir Tripathi |
| 25 |
[GO] |
2023―Sep―29 |
Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein |
Mariem Ghoula, Audrey Deyawe Kongmeneck, Rita Eid, Anne-Claude Camproux, Gautier Moroy |
| 26 |
[GO] |
2023―Sep―28 |
Riding the Wave: Unveiling the Conformational Waves from RBD of SARS-CoV-2 Spike Protein to ACE2 |
Nikhil Maroli |
| 27 |
[GO] |
2023―Sep―27 |
Free Energy Simulations of Receptor-Binding Domain Opening of the SARS-CoV-2 Spike Indicate a Barrierless Transition with Slow Conformational Motions |
Victor Ovchinnikov, Martin Karplus |
| 28 |
[GO] |
2023―Sep―22 |
Intrinsically Disordered Regions Function as a Cervical Collar to Remotely Regulate the Nodding Dynamics of SARS-CoV-2 Prefusion Spike Heads |
Anushree Sinha, Susmita Roy |
| 29 |
[GO] |
2023―Jul―31 |
Comparison and Possible Binding Orientations of SARS-CoV-2 Spike N-Terminal Domain for Gangliosides GM3 and GM1 |
Tanushree Das, Chaitali Mukhopadhyay |
| 30 |
[GO] |
2023―May―17 |
Molecular Insights into the Binding Behavior of Imidazolium Ionic Liquids to the Receptor Binding Domain of the SARS-CoV-2 Spike Protein |
Peng Liu, Yao Li, Yawei Liu, Ju Liu, Kun Dong, Qingzhu Jia |
| 31 |
[GO] |
2023―May―12 |
Adsorption of SARS-CoV-2 Spike (N501Y) RBD to Human Angiotensin-Converting Enzyme 2 at a Lipid/Water Interface |
Harison Rozak, Satoshi Nihonyanagi, Anton Myalitsin, Subhadip Roy, Mohammed Ahmed, Tahei Tahara, Izabela I. Rzeznicka |
| 32 |
[GO] |
2023―Mar―13 |
Biophysical Interpretation of Evolutionary Consequences on the SARS-CoV2 Main Protease through Molecular Dynamics Simulations and Network Topology Analysis |
Nuttawat Sawang, Saree Phongphanphanee, Jirasak Wong-ekkabut, Thana Sutthibutpong |
| 33 |
[GO] |
2023―Feb―24 |
Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization |
Matthew C. Chan, Kui. K. Chan, Erik Procko, Diwakar Shukla |
| 34 |
[GO] |
2023―Feb―15 |
Biophysical Correlates of Enhanced Immunogenicity of a Stabilized Variant of the Receptor Binding Domain of SARS-CoV-2 |
Kawkab Kanjo, Gopinath Chattopadhyay, Sameer Kumar Malladi, Randhir Singh, Sowrabha Jayatheertha, Raghavan Varadarajan |
| 35 |
[GO] |
2023―Jan―23 |
Potential Self-Peptide Inhibitors of the SARS-CoV-2 Main Protease |
Arkadeep Banerjee, Shachi Gosavi |
| 36 |
[GO] |
2022―Oct―11 |
Computational Design and Experimental Validation of ACE2-Derived Peptides as SARS-CoV-2 Receptor Binding Domain Inhibitors |
Sudeep Sarma, Stephanie M. Herrera, Xingqing Xiao, Gregory A. Hudalla, Carol K. Hall |
| 37 |
[GO] |
2022―Sep―30 |
Quantifying Mutational Response to Track the Evolution of SARS-CoV-2 Spike Variants: Introducing a Statistical-Mechanics-Guided Machine Learning Method |
Satyam Sangeet, Raju Sarkar, Saswat K. Mohanty, Susmita Roy |
| 38 |
[GO] |
2022―Sep―06 |
Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule |
Fernando L. Barroso da Silva, Carolina Corrêa Giron, Aatto Laaksonen |
| 39 |
[GO] |
2022―Jul―14 |
All-Atom Simulations of Human ACE2-Spike Protein RBD Complexes for SARS-CoV-2 and Some of its Variants: Nature of Interactions and Free Energy Diagrams for Dissociation of the Protein Complexes |
Saheb Dutta, Bhavana Panthi, Amalendu Chandra |
| 40 |
[GO] |
2022―Jul―12 |
Fast Prediction of Binding Affinities of SARS-CoV-2 Spike Protein and Its Mutants with Antibodies through Intermolecular Interaction Modeling-Based Machine Learning |
Alexander H. Williams, Chang-Guo Zhan |
| 41 |
[GO] |
2022―Jun―23 |
Ionization of D571 Is Coupled with SARS-CoV-2 Spike Up/Down Equilibrium Revealing the pH-Dependent Allosteric Mechanism of Receptor-Binding Domains |
Tong Li, Lan Yu, Jingfang Sun, Jinfeng Liu, Xiao He |
| 42 |
[GO] |
2022―Jun―20 |
SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation |
Hoang Linh Nguyen, Nguyen Quoc Thai, Phuong H. Nguyen, Mai Suan Li |
| 43 |
[GO] |
2022―Jun―06 |
Different Binding Modes of SARS-CoV-1 and SARS-CoV-2 Fusion Peptides to Cell Membranes: The Influence of Peptide Helix Length |
Hujun Shen, Zhenhua Wu, Ling Chen |
| 44 |
[GO] |
2022―May―17 |
Effect of an Amyloidogenic SARS-COV-2 Protein Fragment on α-Synuclein Monomers and Fibrils |
Asis K. Jana, Chance W. Lander, Andrew D. Chesney, Ulrich H. E. Hansmann |
| 45 |
[GO] |
2022―Apr―11 |
Cocktail of REGN Antibodies Binds More Strongly to SARS-CoV-2 Than Its Components, but the Omicron Variant Reduces Its Neutralizing Ability |
Hung Nguyen, Pham Dang Lan, Daniel A. Nissley, Edward P. O’Brien, Mai Suan Li |
| 46 |
[GO] |
2022―Mar―22 |
Generalized Methodology for the Quick Prediction of Variant SARS-CoV-2 Spike Protein Binding Affinities with Human Angiotensin-Converting Enzyme II |
Alexander H. Williams, Chang-Guo Zhan |
| 47 |
[GO] |
2022―Mar―10 |
Combined Computational NMR and Molecular Docking Scrutiny of Potential Natural SARS-CoV-2 Mpro Inhibitors |
Valentin A. Semenov, Leonid B. Krivdin |
| 48 |
[GO] |
2022―Jan―04 |
Detection of Covid-19 through a Heptanal Biomarker Using Transition Metal Doped Graphene |
Anthony Zhu, Xuan Luo |
| 49 |
[GO] |
2021―Dec―14 |
In Silico Elucidation of Potent Inhibitors and Rational Drug Design against SARS-CoV-2 Papain-like Protease |
Kamonpan Sanachai, Panupong Mahalapbutr, Vannajan Sanghiran Lee, Thanyada Rungrotmongkol, Supot Hannongbua |
| 50 |
[GO] |
2021―Sep―27 |
Curious Binding Energy Increase between the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein and Angiotensin-Converting Enzyme 2 Adsorbed on a Silane Monolayer from Molecular Dynamics Simulations |
Solène Lecot, Yann Chevolot, Magali Phaner-Goutorbe, Christelle Yeromonahos |
| 51 |
[GO] |
2021―Sep―21 |
Bioactive Ag3PO4/Polypropylene Composites for Inactivation of SARS-CoV-2 and Other Important Public Health Pathogens |
Lara K. Ribeiro, Marcelo Assis, Lais R. Lima, Dyovani Coelho, Mariana O. Gonçalves, Robert S. Paiva, Leonardo N. Moraes, Lauana F. Almeida, Felipe Lipsky, Miguel A. San-Miguel, Lúcia H. Mascaro, Rejane M. T. Grotto, Cristina P. Sousa, Ieda L. V. Rosa, Sandra A. Cruz, Juan Andrés, Elson Longo |
| 52 |
[GO] |
2021―Aug―09 |
Presence of a SARS-CoV-2 Protein Enhances Amyloid Formation of Serum Amyloid A |
Asis K. Jana, Augustus B. Greenwood, Ulrich H. E. Hansmann |
| 53 |
[GO] |
2021―Jul―30 |
Role of ATP in the RNA Translocation Mechanism of SARS-CoV-2 NSP13 Helicase |
Ryan Weber, Martin McCullagh |
| 54 |
[GO] |
2021―Jul―28 |
Accelerating COVID-19 Research Using Molecular Dynamics Simulation |
Aditya K. Padhi, Soumya Lipsa Rath, Timir Tripathi |
| 55 |
[GO] |
2021―Jul―23 |
Structural Decoding of a Small Molecular Inhibitor on the Binding of SARS-CoV-2 to the ACE 2 Receptor |
Pushpendra Mani Mishra, Chayan Kanti Nandi |
| 56 |
[GO] |
2021―Jul―13 |
Binding of SARS-CoV-2 Fusion Peptide to Host Endosome and Plasma Membrane |
Stefan L. Schaefer, Hendrik Jung, Gerhard Hummer |
| 57 |
[GO] |
2021―Jul―06 |
Electrostatic Interactions Explain the Higher Binding Affinity of the CR3022 Antibody for SARS-CoV-2 than the 4A8 Antibody |
Hung Nguyen, Pham Dang Lan, Daniel A. Nissley, Edward P. O’Brien, Mai Suan Li |
| 58 |
[GO] |
2021―Jun―11 |
Targeting SARS-CoV-2 Receptor Binding Domain with Stapled Peptides: An In Silico Study |
Luana Janaína de Campos, Nicholas Y. Palermo, Martin Conda-Sheridan |
| 59 |
[GO] |
2021―Jun―10 |
Structural and Dynamical Differences in the Spike Protein RBD in the SARS-CoV-2 Variants B.1.1.7 and B.1.351 |
Nisha Bhattarai, Prabin Baral, Bernard S. Gerstman, Prem P. Chapagain |
| 60 |
[GO] |
2021―May―12 |
Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor |
Elhan Taka, Sema Z. Yilmaz, Mert Golcuk, Ceren Kilinc, Umut Aktas, Ahmet Yildiz, Mert Gur |
| 61 |
[GO] |
2021―Apr―30 |
Integrated Biophysical Modeling of the SARS-CoV-2 Spike Protein Binding and Allosteric Interactions with Antibodies |
Gennady M. Verkhivker, Luisa Di Paola |
| 62 |
[GO] |
2021―Apr―23 |
Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates |
Alexander H. Williams, Chang-Guo Zhan |
| 63 |
[GO] |
2021―Mar―03 |
An Active Site Inhibitor Induces Conformational Penalties for ACE2 Recognition by the Spike Protein of SARS-CoV-2 |
Billy J. Williams-Noonan, Nevena Todorova, Ketav Kulkarni, Marie-Isabel Aguilar, Irene Yarovsky |
| 64 |
[GO] |
2021―Jan―15 |
Dynamic Network Modeling of Allosteric Interactions and Communication Pathways in the SARS-CoV-2 Spike Trimer Mutants: Differential Modulation of Conformational Landscapes and Signal Transmission via Cascades of Regulatory Switches |
Gennady M. Verkhivker, Luisa Di Paola |
| 65 |
[GO] |
2020―Dec―02 |
Remdesivir Strongly Binds to Both RNA-Dependent RNA Polymerase and Main Protease of SARS-CoV-2: Evidence from Molecular Simulations |
Hoang Linh Nguyen, Nguyen Quoc Thai, Duc Toan Truong, Mai Suan Li |
| 66 |
[GO] |
2020―Nov―17 |
Computational Design of 25-mer Peptide Binders of SARS-CoV-2 |
Thassanai Sitthiyotha, Surasak Chunsrivirot |
| 67 |
[GO] |
2020―Nov―15 |
Revealing the Inhibition Mechanism of RNA-Dependent RNA Polymerase (RdRp) of SARS-CoV-2 by Remdesivir and Nucleotide Analogues: A Molecular Dynamics Simulation Study |
Padmaja D. Wakchaure, Shibaji Ghosh, Bishwajit Ganguly |
| 68 |
[GO] |
2020―Nov―11 |
How Alcoholic Disinfectants Affect Coronavirus Model Membranes: Membrane Fluidity, Permeability, and Disintegration |
Hossein Eslami, Shubhadip Das, Tianhang Zhou, Florian Müller-Plathe |
| 69 |
[GO] |
2020―Oct―28 |
Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations |
Mahdi Ghorbani, Bernard R. Brooks, Jeffery B. Klauda |
| 70 |
[GO] |
2020―Oct―23 |
Antiviral Peptides as Promising Therapeutics against SARS-CoV-2 |
Surid Mohammad Chowdhury, Shafi Ahmad Talukder, Akib Mahmud Khan, Nadia Afrin, Md Ackas Ali, Rajib Islam, Rimon Parves, Abdulla Al Mamun, Md. Abu Sufian, Md Nayeem Hossain, Mohammed Akhter Hossain, Mohammad A. Halim |
| 71 |
[GO] |
2020―Jul―29 |
Does SARS-CoV-2 Bind to Human ACE2 Stronger Than SARS-CoV? |
Hoang Linh Nguyen, Pham Dang Lan, Nguyen Quoc Thai, Daniel A. Nissley, Edward P. O'Brien, Mai Suan Li |
| 72 |
[GO] |
2020―Jun―19 |
Developing a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein Model in a Viral Membrane |
Hyeonuk Woo, Sang-Jun Park, Yeol Kyo Choi, Taeyong Park, Maham Tanveer, Yiwei Cao, Nathan R. Kern, Jumin Lee, Min Sun Yeom, Tristan Ian Croll, Chaok Seok, Wonpil Im |
| 73 |
[GO] |
2020―Jun―17 |
Critical Differences Between the Binding Features of the Spike Proteins of SARS-CoV-2 and SARS-CoV |
Chen Bai, Arieh Warshel |
| 74 |
[GO] |
2020―Jun―10 |
Structural basis of potential binding mechanism of remdesivir to SARS-CoV-2 RNA dependent RNA polymerase |
Leili Zhang, Ruhong Zhou |
