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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: xiao s. bioRxiv [Preprint]. 2024 May 18:2024.05.17.594786. doi: 10.1101/2024.05.17.594786. bioRxiv. 2024. PMID: 38798650 Free PMC article. Preprint.
Explore Protein Conformational Space With Variational Autoencoder.
Tian H, Jiang X, Trozzi F, Xiao S, Larson EC, Tao P. Tian H, et al. Among authors: xiao s. Front Mol Biosci. 2021 Nov 12;8:781635. doi: 10.3389/fmolb.2021.781635. eCollection 2021. Front Mol Biosci. 2021. PMID: 34869602 Free PMC article.
Machine learning and protein allostery.
Xiao S, Verkhivker GM, Tao P. Xiao S, et al. 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. Among authors: xiao s. 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. 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.
7,683 results