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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: verkhivker 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.
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.
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Raisinghani N, et al. Among authors: verkhivker g. Phys Chem Chem Phys. 2024 Jun 26;26(25):17720-17744. doi: 10.1039/d4cp01372g. Phys Chem Chem Phys. 2024. PMID: 38869513
Atomistic Prediction of Structures, Conformational Ensembles and Binding Energetics for the SARS-CoV-2 Spike JN.1, KP.2 and KP.3 Variants Using AlphaFold2 and Molecular Dynamics Simulations: Mutational Profiling and Binding Free Energy Analysis Reveal Epistatic Hotspots of the ACE2 Affinity and Immune Escape.
Raisinghani N, Alshahrani M, Gupta G, Verkhivker G. Raisinghani N, et al. Among authors: verkhivker g. bioRxiv [Preprint]. 2024 Jul 10:2024.07.09.602810. doi: 10.1101/2024.07.09.602810. bioRxiv. 2024. Update in: Viruses. 2024 Sep 13;16(9):1458. doi: 10.3390/v16091458 PMID: 39026832 Free PMC article. Updated. Preprint.
AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants: Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance.
Raisinghani N, Alshahrani M, Gupta G, Verkhivker G. Raisinghani N, et al. Among authors: verkhivker g. Viruses. 2024 Sep 13;16(9):1458. doi: 10.3390/v16091458. Viruses. 2024. PMID: 39339934 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. Among authors: verkhivker g. Viruses. 2023 Oct 10;15(10):2073. doi: 10.3390/v15102073. Viruses. 2023. PMID: 37896850 Free PMC article.
Prediction of Conformational Ensembles and Structural Effects of State-Switching Allosteric Mutants in the Protein Kinases Using Comparative Analysis of AlphaFold2 Adaptations with Sequence Masking and Shallow Subsampling.
Raisinghani N, Alshahrani M, Gupta G, Tian H, Xiao S, Tao P, Verkhivker G. Raisinghani N, et al. Among authors: verkhivker g. bioRxiv [Preprint]. 2024 May 18:2024.05.17.594786. doi: 10.1101/2024.05.17.594786. bioRxiv. 2024. PMID: 38798650 Free PMC article. Preprint.
151 results