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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.
Microsecond Molecular Dynamics Simulations and Markov State Models of Mutation-Induced Allosteric Mechanisms for the Light-Oxygen-Voltage 2 Protein : Revealing Structural Basis of Signal Transmission Induced by Photoactivation of the Light Protein State.
Xiao S, Ibrahim MT, Verkhivker GM, Zoltowski BD, Tao P. Xiao S, et al. bioRxiv [Preprint]. 2023 Dec 23:2023.12.22.573121. doi: 10.1101/2023.12.22.573121. bioRxiv. 2023. PMID: 38187662 Free PMC article. Preprint.
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.
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: verkhivker g. bioRxiv [Preprint]. 2024 Feb 20:2024.02.15.580591. doi: 10.1101/2024.02.15.580591. bioRxiv. 2024. Update in: J Chem Theory Comput. 2024 Jun 25;20(12):5317-5336. doi: 10.1021/acs.jctc.4c00222. PMID: 38496487 Free PMC article. Updated. Preprint.
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.
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. 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.
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: verkhivker 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.
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: verkhivker g. 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.
153 results