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2021 6
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2023 12
2024 6

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Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and Antibodies: Cooperation of Binding Hotspots in Mediating Epistatic Couplings Underlies Binding Mechanism and Immune Escape.
Raisinghani N, Alshahrani M, Gupta G, Verkhivker G. Raisinghani N, et al. Among authors: gupta g. Int J Mol Sci. 2024 Apr 12;25(8):4281. doi: 10.3390/ijms25084281. Int J Mol Sci. 2024. PMID: 38673865 Free PMC article.
Predicting Functional Conformational Ensembles and Binding Mechanisms of Convergent Evolution for SARS-CoV-2 Spike Omicron Variants Using AlphaFold2 Sequence Scanning Adaptations and Molecular Dynamics Simulations.
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Raisinghani N, et al. Among authors: gupta g. bioRxiv [Preprint]. 2024 Apr 3:2024.04.02.587850. doi: 10.1101/2024.04.02.587850. bioRxiv. 2024. PMID: 38617283 Free PMC article. Preprint.
Interpretable Atomistic Prediction and Functional Analysis of Conformational Ensembles and Allosteric States in Protein Kinases Using AlphaFold2 Adaptation with Randomized Sequence Scanning and Local Frustration Profiling.
Raisinghani N, Alshahrani M, Gupta G, Tian H, Xiao S, Tao P, Verkhivker G. Raisinghani N, et al. Among authors: gupta g. bioRxiv [Preprint]. 2024 Feb 20:2024.02.15.580591. doi: 10.1101/2024.02.15.580591. bioRxiv. 2024. PMID: 38496487 Free PMC article. Preprint.
AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape.
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Raisinghani N, et al. Among authors: gupta g. J Chem Inf Model. 2024 Mar 11;64(5):1657-1681. doi: 10.1021/acs.jcim.3c01857. Epub 2024 Feb 19. J Chem Inf Model. 2024. PMID: 38373700
AlphaFold2-Enabled Atomistic Modeling of Epistatic Binding Mechanisms for the SARS-CoV-2 Spike Omicron XBB.1.5, EG.5 and FLip Variants: Convergent Evolution Hotspots Cooperate to Control Stability and Conformational Adaptability in Balancing ACE2 Binding and Antibody Resistance.
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Raisinghani N, et al. Among authors: gupta g. bioRxiv [Preprint]. 2023 Dec 12:2023.12.11.571185. doi: 10.1101/2023.12.11.571185. bioRxiv. 2023. PMID: 38168257 Free PMC article. Preprint.
Accurate Characterization of Conformational Ensembles and Binding Mechanisms of the SARS-CoV-2 Omicron BA.2 and BA.2.86 Spike Protein with the Host Receptor and Distinct Classes of Antibodies Using AlphaFold2-Augmented Integrative Computational Modeling.
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Raisinghani N, et al. Among authors: gupta g. bioRxiv [Preprint]. 2023 Nov 21:2023.11.18.567697. doi: 10.1101/2023.11.18.567697. bioRxiv. 2023. PMID: 38045395 Free PMC article. Preprint.
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.
24 results