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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.
Verkhivker GM, Agajanian S, Oztas D, Gupta G. Verkhivker GM, et al. Among authors: gupta g. J Biomol Struct Dyn. 2022;40(20):9724-9741. doi: 10.1080/07391102.2021.1933594. Epub 2021 Jun 1. J Biomol Struct Dyn. 2022. PMID: 34060425
Allosteric Control of Structural Mimicry and Mutational Escape in the SARS-CoV-2 Spike Protein Complexes with the ACE2 Decoys and Miniprotein Inhibitors: A Network-Based Approach for Mutational Profiling of Binding and Signaling.
Verkhivker GM, Agajanian S, Oztas DY, Gupta G. Verkhivker GM, et al. Among authors: gupta g. J Chem Inf Model. 2021 Oct 25;61(10):5172-5191. doi: 10.1021/acs.jcim.1c00766. Epub 2021 Sep 22. J Chem Inf Model. 2021. PMID: 34551245
Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies: Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations.
Verkhivker GM, Agajanian S, Oztas DY, Gupta G. Verkhivker GM, et al. Among authors: gupta g. Biochemistry. 2021 May 18;60(19):1459-1484. doi: 10.1021/acs.biochem.1c00139. Epub 2021 Apr 26. Biochemistry. 2021. PMID: 33900725
Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms.
Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. Xiao S, et al. Among authors: gupta g. J Chem Inf Model. 2023 Aug 28;63(16):5272-5296. doi: 10.1021/acs.jcim.3c00778. Epub 2023 Aug 7. J Chem Inf Model. 2023. PMID: 37549201
Comparative Analysis of Conformational Dynamics and Systematic Characterization of Cryptic Pockets in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 Spike Complexes with the ACE2 Host Receptor: Confluence of Binding and Structural Plasticity in Mediating Networks of Conserved Allosteric Sites.
Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Alshahrani M, et al. Among authors: gupta g. Viruses. 2023 Oct 10;15(10):2073. doi: 10.3390/v15102073. Viruses. 2023. PMID: 37896850 Free PMC article.
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