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The Royal Society of Chemistry: Physical Chemistry Chemical Physics
  original article Date Title Authors   All Authors
1 [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
2 [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
3 [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
4 [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
5 [GO] 2024―Feb―02 Allosteric Regulation in SARS-CoV-2 Spike Protein Yong Wei, Amy Chen, Yuewei Lin, Tao Wei, Baofu Qiao
6 [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
7 [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
8 [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
9 [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
10 [GO] 2023―Aug―22 Binding of synthetic nanobodies to SARS-CoV-2 receptor-binding domain: the importance of salt bridge Hujun Shen, Hengxiu Yang
11 [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
12 [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
13 [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
14 [GO] 2023―May―15 The SARS-CoV-2 spike protein structure: a symmetry tale on distortion trail Inbal Tuvi-Arad, Yaffa Shalit
15 [GO] 2023―Apr―12 Molecular dynamics simulations of SARS-CoV-2 main protease and potential inhibitors Xingyu Li, Zhou Fang, Dechang Li, Zhenhai Li
16 [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
17 [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
18 [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
19 [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
20 [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
21 [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)
22 [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
23 [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
24 [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
25 [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
26 [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
27 [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
28 [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
29 [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
30 [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
31 [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
32 [GO] 2022―Jun―20 In silico study on the effects of disulfide bonds in ORF8 of SARS-CoV-2 Yadi Cheng, Xubiao Peng
33 [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
34 [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
35 [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
36 [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
37 [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
38 [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)
39 [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)
40 [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
41 [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
42 [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)
43 [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
44 [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)
45 [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)
46 [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
47 [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
48 [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
49 [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
50 [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
51 [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)
52 [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
53 [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
54 [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
55 [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
56 [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
57 [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

57 Results       Page 1


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