Sian Xiao

Publication Activity (10 Years)

Years Active: 2022-2024
Publications (10 Years): 41

Top Topics

Molecular Dynamics Simulations

Machine Learning

Top Venues

bioRxiv : the preprint server for biology

Journal of chemical information and modeling

Physical chemistry chemical physics : PCCP

The journal of physical chemistry. B

This page only lists publications with an associated author ORCID identifier.

Publications

Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. bioRxiv : the preprint server for biology (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. bioRxiv : the preprint server for biology (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. Physical chemistry chemical physics : PCCP 26 (25) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
Integration of a Randomized Sequence Scanning Approach in AlphaFold2 and Local Frustration Profiling of Conformational States Enable Interpretable Atomistic Characterization of Conformational Ensembles and Detection of Hidden Allosteric States in the ABL1 Protein Kinase. Journal of chemical theory and computation 20 (12) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. Physical chemistry chemical physics : PCCP (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. bioRxiv : the preprint server for biology (2024)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. Journal of computational chemistry (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. bioRxiv : the preprint server for biology (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. Journal of chemical information and modeling 64 (5) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. Journal of chemical information and modeling 64 (5) (2024)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. Journal of computational chemistry 45 (17) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between Convergent Mutational Hotspots that Control ACE2 Affinity. The journal of physical chemistry. B 128 (19) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. bioRxiv : the preprint server for biology (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between Convergent Mutational Hotspots that Control ACE2 Affinity. The journal of physical chemistry. B 128 (19) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. Physical chemistry chemical physics : PCCP (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between Convergent Mutational Hotspots that Control ACE2 Affinity. The journal of physical chemistry. B (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. Journal of chemical information and modeling (2024)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. Journal of computational chemistry 45 (17) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. Physical chemistry chemical physics : PCCP 26 (25) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
Integration of a Randomized Sequence Scanning Approach in AlphaFold2 and Local Frustration Profiling of Conformational States Enable Interpretable Atomistic Characterization of Conformational Ensembles and Detection of Hidden Allosteric States in the ABL1 Protein Kinase. Journal of chemical theory and computation (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. Journal of chemical information and modeling 64 (5) (2024)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. Journal of computational chemistry 45 (17) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. bioRxiv : the preprint server for biology (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
Integration of a Randomized Sequence Scanning Approach in AlphaFold2 and Local Frustration Profiling of Conformational States Enable Interpretable Atomistic Characterization of Conformational Ensembles and Detection of Hidden Allosteric States in the ABL1 Protein Kinase. Journal of chemical theory and computation (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
Integration of a Randomized Sequence Scanning Approach in AlphaFold2 and Local Frustration Profiling of Conformational States Enable Interpretable Atomistic Characterization of Conformational Ensembles and Detection of Hidden Allosteric States in the ABL1 Protein Kinase. Journal of chemical theory and computation 20 (12) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. bioRxiv : the preprint server for biology (2024)
Sian Xiao, Mohammed Alshahrani, Grace Gupta, Peng Tao, Gennady M Verkhivker
Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. Journal of chemical information and modeling (2023)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
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. bioRxiv : the preprint server for biology (2023)
Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. Viruses 15 (10) (2023)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. bioRxiv : the preprint server for biology (2023)
Gennady M Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao
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. bioRxiv : the preprint server for biology (2023)
Gennady M Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao
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. Physical chemistry chemical physics : PCCP (2023)
Gennady M Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao
From Deep Mutational Mapping of Allosteric Protein Landscapes to Deep Learning of Allostery and Hidden Allosteric Sites: Zooming in on "Allosteric Intersection" of Biochemical and Big Data Approaches. International journal of molecular sciences 24 (9) (2023)
Gennady M Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao
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. bioRxiv : the preprint server for biology (2023)
Gennady M Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao
From Deep Mutational Mapping of Allosteric Protein Landscapes to Deep Learning of Allostery and Hidden Allosteric Sites: Zooming in on "Allosteric Intersection" of Biochemical and Big Data Approaches. International journal of molecular sciences 24 (9) (2023)
Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes. bioRxiv : the preprint server for biology (2023)
Hao Tian, Sian Xiao, Xi Jiang, Peng Tao
PASSer: fast and accurate prediction of protein allosteric sites. Nucleic acids research (2023)
Sian Xiao, Mohammed Alshahrani, Grace Gupta, Peng Tao, Gennady M Verkhivker
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. bioRxiv : the preprint server for biology (2023)
Haoxiang Li, Hao Tian, Yewei Chen, Sian Xiao, Xiu-Ying Zhao, Yangyang Gao, Liqun Zhang
Analyzing and Predicting the Viscosity of Polymer Nanocomposites in the Conditions of Temperature, Shear Rate, and Nanoparticle Loading with Molecular Dynamics Simulations and Machine Learning. The journal of physical chemistry. B (2023)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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. bioRxiv : the preprint server for biology (2023)
Hao Tian, Xi Jiang, Sian Xiao, Hunter La Force, Eric C Larson, Peng Tao
LAST: Latent Space-Assisted Adaptive Sampling for Protein Trajectories. Journal of chemical information and modeling (2022)