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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. Among authors: verkhivker gm. bioRxiv [Preprint]. 2023 Dec 23:2023.12.22.573121. doi: 10.1101/2023.12.22.573121. bioRxiv. 2023. PMID: 38187662 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. 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 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. bioRxiv [Preprint]. 2023 Dec 12:2023.12.11.571185. doi: 10.1101/2023.12.11.571185. bioRxiv. 2023. PMID: 38168257 Free PMC article. Preprint.
Machine learning and protein allostery.
Xiao S, Verkhivker GM, Tao P. Xiao S, et al. Among authors: verkhivker gm. Trends Biochem Sci. 2023 Apr;48(4):375-390. doi: 10.1016/j.tibs.2022.12.001. Epub 2022 Dec 21. Trends Biochem Sci. 2023. PMID: 36564251 Free PMC article. Review.
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. PMID: 37205479 Free PMC article. Updated. Preprint.
138 results