Mohammed Alshahrani

Publication Activity (10 Years)

Years Active: 2023-2024
Publications (10 Years): 23

Top Topics

Molecular Dynamics Simulations

Network Analysis

Top Venues

bioRxiv : the preprint server for biology

International journal of molecular sciences

Physical chemistry chemical physics : PCCP

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, 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)
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, Gennady M Verkhivker
Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and Antibodies: Cooperation of Binding Hotspots in Mediating Epistatic Couplings Underlies Binding Mechanism and Immune Escape. International journal of molecular sciences 25 (8) (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
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, Gennady M Verkhivker
Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and Antibodies: Cooperation of Binding Hotspots in Mediating Epistatic Couplings Underlies Binding Mechanism and Immune Escape. International journal of molecular sciences 25 (8) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Gennady M Verkhivker
Ensemble-Based Mutational Profiling and Network Analysis of the SARS-CoV-2 Spike Omicron XBB Lineages for Interactions with the ACE2 Receptor and Antibodies: Cooperation of Binding Hotspots in Mediating Epistatic Couplings Underlies Binding Mechanism and Immune Escape. International journal of molecular sciences 25 (8) (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
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
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)
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)
Gennady M Verkhivker, Mohammed Alshahrani, Grace Gupta
Exploring Conformational Landscapes and Cryptic Binding Pockets in Distinct Functional States of the SARS-CoV-2 Omicron BA.1 and BA.2 Trimers: Mutation-Induced Modulation of Protein Dynamics and Network-Guided Prediction of Variant-Specific Allosteric Binding Sites. Viruses 15 (10) (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
Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes. Viruses 15 (5) (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
Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers: Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants. International journal of molecular sciences 24 (7) (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)
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)