| |
original article |
Date |
Title |
Authors All Authors |
| 1 |
[GO] |
2025―Mar―04 |
Unraveling the impact of binary vs ternary alcohol solutions on the conformation and solvation of the SARS-CoV-2 receptor- binding domain |
Rabiul Gazi, Madhurima Jana |
| 2 |
[GO] |
2024―Nov―22 |
Molecular Insights into Dalbavancin’s Blockade of ACE2-Spike Protein Interaction in SARS-CoV-2 |
Zhongbo Liu, Yuxi Lv, Song Luo, Lili Duan |
| 3 |
[GO] |
2024―Nov―21 |
SARS-CoV-2 Variants and Bebtelovimab: Immune Escape Mechanisms Revealed by Computational Studies |
Rakesh Kumar Roy, Madhur Sharma, Niladri Patra |
| 4 |
[GO] |
2024―Oct―02 |
The critical role of aromatic residues in the binding of the SARS-CoV-2 fusion peptide to phospholipid bilayer membrane |
Hujun Shen, Ling Chen, Hengxiu Yang |
| 5 |
[GO] |
2024―Jun―10 |
Exploring Conformational Landscapes and Binding Mechanisms of Convergent Evolution for the SARS-CoV-2 Spike Omicron Variant Complexes with the ACE2 Receptor Using AlphaFold2-Based Structural Ensembles and Molecular Dynamics Simulations |
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker |
| 6 |
[GO] |
2024―Apr―16 |
Interface design of SARS-CoV-2 symmetrical nsp7 dimer and machine learning-guided nsp7 sequence prediction reveals physicochemical properties and hotspots for nsp7 stability, adaptation, and therapeutic design |
Amar Jeet Yadav, Shivank Kumar, Shweata Maurya, Khushboo Bhagat, Aditya Padhi |
| 7 |
[GO] |
2024―Mar―12 |
Can Duvelisib and Eganelisib Work for both Cancer and COVID-19? Molecular-level Insights from MD Simulations and Enhanced Samplings |
Saroj Kumar Panda, Shaswata Karmakar, Parth Sarthi Sen Gupta, Malay Kumar Rana |
| 8 |
[GO] |
2024―Feb―22 |
Insights from In Silico Study of Receptor Energetics of SARS-CoV-2 Variants |
Lokendra Singh Dhami, Prabin Dahal, Bidhya Thapa, Narayan Gautam, Nurapati Pantha, Rameshwar Adhikari, Narayan Prasad Adhikari |
| 9 |
[GO] |
2024―Feb―02 |
Allosteric Regulation in SARS-CoV-2 Spike Protein |
Yong Wei, Amy Chen, Yuewei Lin, Tao Wei, Baofu Qiao |
| 10 |
[GO] |
2024―Jan―25 |
Interaction of III-As Monolayer with SARS-CoV-2 Biomarkers: Implications for Biosensor Development |
Sudipta Saha, Deb Indronil Sajib, Md Kawsar Alam |
| 11 |
[GO] |
2023―Dec―11 |
Trapping non-cognate nucleotide upon initial binding for replication fidelity control in SARS-CoV-2 RNA dependent RNA polymerase |
Moises Ernesto Romero, Shannon J McElhenney, Jin Yu |
| 12 |
[GO] |
2023―Sep―12 |
Computational Study on the Mechanisms of Inhibition of SARS-CoV-2 Mpro by Aldehyde Warhead Based on DFT |
Yongsheng Yang, Chenghua Zhang, Xingcan Qian, Feiyun Jia, Shiwei Liang |
| 13 |
[GO] |
2023―Aug―22 |
Molecular Mechanism of Non-covalent Inhibitor WU-04 Targeting SARS-CoV-2 3CLpro and Computational Evaluation of Its Effectiveness Against Mainstream Coronaviruses |
Jianhua Wu, Hong-Xing Zhang, Ji-Long Zhang |
| 14 |
[GO] |
2023―Aug―22 |
Binding of synthetic nanobodies to SARS-CoV-2 receptor-binding domain: the importance of salt bridge |
Hujun Shen, Hengxiu Yang |
| 15 |
[GO] |
2023―Aug―02 |
Probing Conformational Landscapes of Binding and Allostery in the SARS-CoV-2 Omicron Variant Complexes Using Microsecond Atomistic Simulations and Perturbation-Based Profiling Approaches: Hidden Role of Omicron Mutations as Modulators of Allosteric Signaling and Epistatic Relationships |
Gennady M Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao |
| 16 |
[GO] |
2023―May―18 |
In silico design of miniprotein to inhibit SARS-CoV-2 variant Omicron spike protein |
Jianhua Wu, Hong-Xing Zhang, Jilong Zhang |
| 17 |
[GO] |
2023―May―15 |
The Molecular Mechanism Study of Structural Regulation of the N-terminal Domain Binding Antibody on the Receptor Binding Domain of SARS-CoV-2 |
Liu Hongtao, Zihui Tian, Shuai Yuan, Shuangyan Zhou |
| 18 |
[GO] |
2023―May―15 |
The SARS-CoV-2 spike protein structure: a symmetry tale on distortion trail |
Inbal Tuvi-Arad, Yaffa Shalit |
| 19 |
[GO] |
2023―Apr―12 |
Molecular dynamics simulations of SARS-CoV-2 main protease and potential inhibitors |
Xingyu Li, Zhou Fang, Dechang Li, Zhenhai Li |
| 20 |
[GO] |
2023―Apr―12 |
Energetic vs entropic stabilization between Remdesivir analogue and cognate ATP upon binding and insertion into active site of SARS-CoV-2 RNA dependent RNA polymerase |
Chunhong Long, Moises Ernesto Romero, Liqiang Dai, Jin Yu |
| 21 |
[GO] |
2023―Apr―06 |
Development of Multiscale Ultra-Coarse-Grained Models for the SARS-CoV-2 Virion from Cryo-Electron Microscopy Data |
Fengyu Li, Yuwei Zhang, Fei Xia, Xin Xu |
| 22 |
[GO] |
2023―Feb―14 |
Membrane Cholesterol Regulates the Oligomerization and Fusogenicity of SARS-CoV Fusion Peptide: Implications in Viral Entry |
Geetanjali Meher, Surajit Bhattacharjya, Hirak Chakraborty |
| 23 |
[GO] |
2023―Jan―04 |
Investigation on the interaction mechanism of different SARS-CoV-2 spike variants with hACE2: insights from molecular dynamics simulations |
Jianhua Wu, Hong-Xing Zhang, Jilong Zhang |
| 24 |
[GO] |
2022―Dec―13 |
Correction: Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches |
Son Tung Ngo, Trung Hai Nguyen, Nguyen Thanh Tung, Van V. Vue, Minh Quan Pham, Binh Khanh Mai |
| 25 |
[GO] |
2022―Nov―21 |
Optimization of Potential Non-covalent Inhibitors for SARS-CoV-2 Main Protease Inspected by a Descriptor of Subpocket Occupancy |
Yujia Sun, Bodi Zhao, Yuqi Wang, Zitong Chen, Lingbo Qu, Huaiyu Zhang, et al. (+2) Yuan Zhao, Jinshuai Song |
| 26 |
[GO] |
2022―Nov―15 |
Characterizing the ligand-binding affinity to SARS-CoV-2 Mpro via physics and knowledge based approaches |
Son Tung Ngo, Trung Hai Nguyen, Nguyen Thanh Tung, Van V. Vu, Minh Quan Pham, Binh Khanh Mai |
| 27 |
[GO] |
2022―Oct―25 |
Correction: Computational investigation of the increased virulence and pathogenesis of SARS-CoV-2 lineage B.1.1.7 |
N. Arul Murugan, Prashanth S. Javali, Chitra Jeyaraj Pandianb, Muhammad Akhtar Ali, Vaibhav Srivastava, Jeyakanthan Jeyaraman |
| 28 |
[GO] |
2022―Oct―25 |
Biological effect of black phosphorus nanosheets to the interaction between SARS-CoV-2 S protein and ACE2 |
Ruirui Liu, Hong Lin Zhai, Hai Ping Shao, Tian Hua Wang |
| 29 |
[GO] |
2022―Oct―04 |
Proof-of-concept Study of the Secondary Structure of Influenza A, B M2, and MERS-, SARS-CoV E Transmembrane Peptides Using Folding Molecular Dynamics Simulations in Membrane Mimetic Solvent |
Antonios Kolocouris, Isaiah T. Arkin, Nicholas M Glykos |
| 30 |
[GO] |
2022―Sep―14 |
RBD spatial orientation of the spike protein and its binding to ACE2: insight into high infectivity of SARS-CoV-2 Delta variant from MD simulations |
Nan Lv, Zexing Cao |
| 31 |
[GO] |
2022―Sep―14 |
Estimating the Binding Energetics of Reversible Covalent Inhibitors of the SARS-CoV-2 Main Protease: An in-silico study |
Ernest Awoonor-Williams |
| 32 |
[GO] |
2022―Sep―14 |
Structural Insights Into Nirmatrelvir (PF-07321332)-3C-like SARS-CoV-2 Protease Complexation: A Ligand Gaussian Accelerated Molecular Dynamics Study |
Yeng-Tseng Wang, Jun-min Liao, Wen-Wei Lin, Chia-Ching Li, Bo-Cheng Huang, Tian-Lu Cheng, Tun-Chieh Chen |
| 33 |
[GO] |
2022―Aug―30 |
Deciphering binding mechanism of inhibitors to SARS-COV-2 main protease through multiple replica accelerated molecular dynamics simulations and free energy landscapes |
Meng Li, Xinguo Liu, Shaolong Zhang, Shanshan Liang, Qinggang Zhang, Jianzhong Chen |
| 34 |
[GO] |
2022―Aug―02 |
Computational Investigation of Increased Virulence and Pathogenesis of SARS-CoV-2 Lineage B.1.1.7 |
Arul Murugan Natarajan, Prashanth S. Javali, Chitra jeyarajpandian, Muhammad Akhtar Ali, Vaibhav Srivastava, Jeyakanthan Jeyaraman |
| 35 |
[GO] |
2022―Jul―12 |
Frustration-Driven Allosteric Regulation and Signal Transmission in the SARS-CoV-2 Spike Omicron Trimer Structures: A Crosstalk of the Omicron Mutation Sites Allosterically Regulates Tradeoffs of Protein Stability and Conformational Adaptability |
Gennady M Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan |
| 36 |
[GO] |
2022―Jun―20 |
In silico study on the effects of disulfide bonds in ORF8 of SARS-CoV-2 |
Yadi Cheng, Xubiao Peng |
| 37 |
[GO] |
2022―Apr―01 |
High-throughput Designing of Symmetrical Dimeric SARS-CoV-2 Main Protease: Structural and Physical Insights into Hotspots for Adaptation and Therapeutics |
Aditya K Padhi, Timir Tripathi |
| 38 |
[GO] |
2022―Mar―30 |
Significance of the RBD mutations in the SARS-CoV-2 Omicron: from spike opening to antibody escape and cell attachment |
Md Lokman Hossen, Prabin Baral, Tej Sharma, Bernard S Gerstman, Prem Chapagain |
| 39 |
[GO] |
2022―Mar―21 |
Insights from computational analysis: how does the SARS-CoV-2 Delta (B.1.617.2) variant hijack ACE2 more effectively? |
Danyang Xiong, Xiaoyu Zhao, Song Luo, Lili Duan |
| 40 |
[GO] |
2022―Feb―08 |
Exploring the Permeability of Covid-19 Drugs within the Cellular Membrane: A Molecular Dynamics Simulation Study |
Tahereh Ghaed-sharaf, Akbar Omidvar |
| 41 |
[GO] |
2022―Jan―28 |
Grammatical Evolution-based design of the SARS-CoV-2 main protease inhibitors |
Francisco Frausto-Parada, Ismael Várgas-Rodríguez, Itzel Marcado-Sánchez, Adán Bazán-Jiménez, Erik Díaz-Cervantes, Marco Aurelio Sotelo-Figueroa, Marco Antonio García-Revilla |
| 42 |
[GO] |
2022―Jan―18 |
Structural and Energetic Features of the Dimerization of SARS-CoV-2 Main Proteinase from Molecular Dynamic Simulations |
Yunju Zhang, Liangzhen Zheng, Yanmei Yang, Yuanyuan Qu, Yong-Qiang Li, Mingwen Zhao, et al. (+2) Yuguang Mu, Weifeng Li |
| 43 |
[GO] |
2022―Jan―12 |
Predicting spike protein NTD mutations of SARS-CoV-2 causing immune escape by molecular dynamics simulations |
Liping Zhou, Leyun Wu, Cheng Peng, Yanqing Yang, Yulong Shi, Likun Gong, et al. (+2) Zhijian Xu, Weiliang Zhu |
| 44 |
[GO] |
2021―Dec―17 |
Binding mechanism of inhibitors to SARS-CoV-2 main protease deciphered by multiple replica molecular dynamics simulations |
Shanshan Liang, Xinguo Liu, Shaolong Zhang, Meng Li, Qinggang Zhang, Jianzhong Chen |
| 45 |
[GO] |
2021―Nov―04 |
Mechanistic Insights into the Effects of Key Mutations on SARS-CoV-2 RBD-ACE2 Binding |
Abhishek Aggarwal, Supriyo Naskar, Nikhil Maroli, Biswajit Gorai, Narendra M. Dixit, Prabal Kumar Maiti |
| 46 |
[GO] |
2021―Oct―05 |
Microscopic interactions between ivermectin and key human and viral proteins involved in SARS-CoV-2 infection |
Antonio Francés-Monerris, Cristina Garcia Iriepa, Isabel Iriepa, Cécilia Hognon, Tom Miclot, Giampaolo Barone, et al. (+2) Antonio Monari, Marco Marazzi |
| 47 |
[GO] |
2021―Sep―06 |
Incorporation Efficiency and Inhibition Mechanism of 2’-Substituted Nucleotide Analogs against SARS-CoV-2 RNA-dependent RNA polymerase |
Congmin Yuan, Eshani C. Goonetilleke, Ilona Christy Unarta, Xuhui Huang |
| 48 |
[GO] |
2021―Jun―28 |
Corilagin and 1,3,6-Tri-O-galloyl-β-D-glucose: Potential inhibitors of SARS-CoV-2 Variants |
Vincent Binette, Sébastien Côté, Mohamed Hadded, Phuong Trang Nguyen, Sébastien Bélanger, Roger Gaudreault, et al. (+3) Steve Bourgault, Charles Ramassamy, Normand Mousseau |
| 49 |
[GO] |
2021―Jun―03 |
Molecular insights into the binding variance of SARS-CoV-2 spike with human, cat and dog ACE2 proteins |
Yongjian Zang, Xuhua Li, Yizhen Zhao, He Wang, Dongxiao Hao, Lei Zhang, et al. (+3) Zhiwei Yang, Xiaohui Yuan, Shengli Zhang |
| 50 |
[GO] |
2021―May―28 |
Quantitative analysis of ACE2 bindings to coronavirus spike proteins：SARS-CoV-2 vs SARS-CoV and RaTG13 |
Zhendong Li, John Z.H. Zhang |
| 51 |
[GO] |
2021―May―28 |
Correction: Antiviral drug design based on the opening mechanism of spike glycoprotein in SARS-CoV-2 |
Ruichao Mao, Lihua Bie, Maofeng Xu, Xiaocong Wang, Jun Gao |
| 52 |
[GO] |
2021―May―03 |
Antiviral Drug Design Based on the Opening Mechanism of Spike Glycoprotein in SARS-CoV-2 |
Ruichao Mao, Lihua Bie, Maofeng Xu, Xiaocong Wang, Jun Gao |
| 53 |
[GO] |
2021―Mar―10 |
Crystallography based investigation of weak interaction for drug designing against COVID-19 |
Nayim Sepay, Pranab C. Saha, Zarrin Shahzadi, Aratrika Chakraborty, Umesh Chandra Halder |
| 54 |
[GO] |
2021―Mar―09 |
Covalent and Non-Covalent Binding Free Energy Calculations for Peptidomimetic Inhibitors of SARS-CoV-2 Main Protease |
Ernest Awoonor-Williams, Abd Al-Aziz A Abu-Saleh |
| 55 |
[GO] |
2021―Feb―19 |
1’-Ribose Cyano Substitution Allows Remdesivir to Effectively Inhibit Nucleotide Addition and Proofreading during SARS-CoV-2 Viral RNA Replication |
Lu Zhang, Dong Zhang, Xiaowei Wang, Congmin Yuan, Yongfang Li, Xilin Jia, et al. (+4) Xin Gao, Hui-Ling Yen, Peter Pak-Hang Cheung, Xuhui Huang |
| 56 |
[GO] |
2020―Nov―19 |
Role of Different Tautomers on the Base-Pairing Abilities of Some of the Vital Antiviral Drugs used Against COVID-19 |
Nihar R Jena |
| 57 |
[GO] |
2020―Nov―12 |
Tracing driving forces responsible for the remarkable infectivity of 2019-nCoV: 1. receptor binding domain in its bound and unbound states |
Ziyi Liu, Miaoren Xia, Zhifang Chai, Dongqi Wang |
| 58 |
[GO] |
2020―Oct―26 |
Structure-Based Lead Optimization of Herbal Medicine Rutin for Inhibiting SARS-CoV-2's Main Protease |
Tien Huynh, Haoran Wang, Binquan Luan |
| 59 |
[GO] |
2020―Sep―21 |
Discovery of Potent Inhibitors for SARS-CoV-2’s Main Protease by Ligand-based/Structure-based Virtual Screening, MD Simulations, and Binding Energy Calculations. |
Abd Al-Aziz A Abu-Saleh, Ibrahim E E. Awad, Arpita Yadav, Ray Poirier |
| 60 |
[GO] |
2020―Aug―13 |
Dynamical properties of enzyme-substrate complexes disclose substrate specificity of the SARS-CoV-2 main protease as characterized by the electron density descriptors |
Maria Khrenova, Vladimir G. Tsirelson, Alexander Nemukhin |
| 61 |
[GO] |
2020―Aug―05 |
Intra- and intermolecular atomic-scale interactions in the receptor binding domain of SARS-CoV-2 spike protein: implication for ACE2 receptor binding |
Puja Adhikari, Neng Li, Matthew Shin, Nicole F. Steinmetz, Reidun Twarock, Rudolf Podgornik, Wai-Yim Ching |
