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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.
Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Verkhivker G, et al. Among authors: alshahrani m. bioRxiv [Preprint]. 2023 May 4:2023.05.03.539337. doi: 10.1101/2023.05.03.539337. bioRxiv. 2023. Update in: Phys Chem Chem Phys. 2023 Aug 16;25(32):21245-21266. doi: 10.1039/d3cp02042h PMID: 37205479 Free PMC article. Updated. Preprint.
Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variants 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: alshahrani m. bioRxiv [Preprint]. 2023 May 22:2023.05.20.541592. doi: 10.1101/2023.05.20.541592. bioRxiv. 2023. Update in: J Chem Inf Model. 2023 Aug 28;63(16):5272-5296. doi: 10.1021/acs.jcim.3c00778 PMID: 37292827 Free PMC article. Updated. Preprint.
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.
Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Verkhivker G, et al. Among authors: alshahrani m. Phys Chem Chem Phys. 2023 Aug 16;25(32):21245-21266. doi: 10.1039/d3cp02042h. Phys Chem Chem Phys. 2023. PMID: 37548589 Free PMC article.
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: alshahrani m. 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 Free PMC article.
Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes.
Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Alshahrani M, et al. bioRxiv [Preprint]. 2023 Sep 12:2023.09.11.557205. doi: 10.1101/2023.09.11.557205. bioRxiv. 2023. PMID: 37745525 Free PMC article. Preprint.
Exploring Conformational Landscapes and Cryptic Binding Pockets in Distinct Functional States of the SARS-CoV-2 Omicron BA.1 and BA.2 Trimers: Mutation-Induced Modulation of Protein Dynamics and Network-Guided Prediction of Variant-Specific Allosteric Binding Sites.
Verkhivker G, Alshahrani M, Gupta G. Verkhivker G, et al. Among authors: alshahrani m. Viruses. 2023 Sep 27;15(10):2009. doi: 10.3390/v15102009. Viruses. 2023. PMID: 37896786 Free PMC article.
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. Viruses. 2023 Oct 10;15(10):2073. doi: 10.3390/v15102073. Viruses. 2023. PMID: 37896850 Free PMC article.
637 results