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For: Halder A, Anto A, Subramanyan V, Bhattacharyya M, Vishveshwara S, Vishveshwara S. Surveying the Side-Chain Network Approach to Protein Structure and Dynamics: The SARS-CoV-2 Spike Protein as an Illustrative Case. Front Mol Biosci 2020;7:596945. [PMID: 33392257 PMCID: PMC7775578 DOI: 10.3389/fmolb.2020.596945] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/04/2020] [Indexed: 02/04/2023]  Open
Number Cited by Other Article(s)
1
Mahapatra S, Kar P. Computational Biophysical Characterization of the Effect of Gatekeeper Mutations on the Binding of Ponatinib to the FGFR Kinase. Arch Biochem Biophys 2024:110070. [PMID: 38909834 DOI: 10.1016/j.abb.2024.110070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/15/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
2
Franke L, Peter C. Visualizing the Residue Interaction Landscape of Proteins by Temporal Network Embedding. J Chem Theory Comput 2023;19:2985-2995. [PMID: 37122117 DOI: 10.1021/acs.jctc.2c01228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
3
Manrique PD, Chakraborty S, Henderson R, Edwards RJ, Mansbach R, Nguyen K, Stalls V, Saunders C, Mansouri K, Acharya P, Korber B, Gnanakaran S. Network analysis uncovers the communication structure of SARS-CoV-2 spike protein identifying sites for immunogen design. iScience 2023;26:105855. [PMID: 36590900 PMCID: PMC9791713 DOI: 10.1016/j.isci.2022.105855] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/17/2022] [Accepted: 12/19/2022] [Indexed: 12/27/2022]  Open
4
Verkhivker GM, Agajanian S, Oztas D, Gupta G. Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation. J Biomol Struct Dyn 2022;40:9724-9741. [PMID: 34060425 DOI: 10.1080/07391102.2021.1933594] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
5
Lata S, Akif M. Probing structural basis for enhanced binding of SARS-CoV-2 P.1 variant spike protein with the human ACE2 receptor. J Cell Biochem 2022;123:1207-1221. [PMID: 35620980 PMCID: PMC9347910 DOI: 10.1002/jcb.30276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/22/2022] [Accepted: 05/10/2022] [Indexed: 11/25/2022]
6
Behbahani M, Mohabatkar H, Hosseini B. In silico design of quadruplex aptamers against the spike protein of SARS-CoV-2. INFORMATICS IN MEDICINE UNLOCKED 2021;26:100757. [PMID: 34664030 PMCID: PMC8514331 DOI: 10.1016/j.imu.2021.100757] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 12/24/2022]  Open
7
Verkhivker GM, Agajanian S, Oztas DY, Gupta G. Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. ACS OMEGA 2021;6:16216-16233. [PMID: 34179666 PMCID: PMC8223427 DOI: 10.1021/acsomega.1c02336] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/01/2021] [Indexed: 05/05/2023]
8
Kumari A, Mittal L, Srivastava M, Asthana S. Binding mode characterization of 13b in the monomeric and dimeric states of SARS-CoV-2 main protease using molecular dynamics simulations. J Biomol Struct Dyn 2021;40:9287-9305. [PMID: 34029506 DOI: 10.1080/07391102.2021.1927844] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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