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Works (10)

Mutational Scanning and Binding Free Energy Computations of the SARS-CoV-2 Spike Complexes with Distinct Groups of Neutralizing Antibodies: Energetic Drivers of Convergent Evolution of Binding Affinity and Immune Escape Hotspots

International Journal of Molecular Sciences
2025-02 | Journal article | Author
DOI: 10.3390/ijms26041507
Contributors: Mohammed Alshahrani; Vedant Parikh; Brandon Foley; Nishank Raisinghani; Gennady Verkhivker
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Multidisciplinary Digital Publishing Institute

Quantitative Characterization and Prediction of the Binding Determinants and Immune Escape Hotspots for Groups of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling of the SARS-CoV-2 Spike Complexes with Antibodies

Biomolecules
2025-02 | Journal article | Author
DOI: 10.3390/biom15020249
Contributors: Mohammed Alshahrani; Vedant Parikh; Brandon Foley; Nishank Raisinghani; Gennady Verkhivker
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Multidisciplinary Digital Publishing Institute

AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants: Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance

Viruses
2024-09 | Journal article | Author
DOI: 10.3390/v16091458
Contributors: Nishank Raisinghani; Mohammed Alshahrani; Grace Gupta; Gennady Verkhivker
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Multidisciplinary Digital Publishing Institute

Predicting Mutation-Induced Allosteric Changes in Structures and Conformational Ensembles of the ABL Kinase Using AlphaFold2 Adaptations with Alanine Sequence Scanning

International Journal of Molecular Sciences
2024-09 | Journal article | Author
DOI: 10.3390/ijms251810082
Contributors: Nishank Raisinghani; Mohammed Alshahrani; Grace Gupta; Gennady Verkhivker
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Multidisciplinary Digital Publishing Institute

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
2024-04 | Journal article | Author
DOI: 10.3390/ijms25084281
Contributors: Nishank Raisinghani; Mohammed Alshahrani; Grace Gupta; Gennady Verkhivker
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Multidisciplinary Digital Publishing Institute

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
2023-10 | Journal article | Author
DOI: 10.3390/v15102073
Contributors: Mohammed Alshahrani; Grace Gupta; Sian Xiao; Peng Tao; Gennady Verkhivker
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Multidisciplinary Digital Publishing Institute

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
2023-09 | Journal article | Author
DOI: 10.3390/v15102009
Contributors: Gennady Verkhivker; Mohammed Alshahrani; Grace Gupta
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Multidisciplinary Digital Publishing Institute

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
2023-04 | Journal article | Author
DOI: 10.3390/ijms24076642
Contributors: Gennady Verkhivker; Mohammed Alshahrani; Grace Gupta
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Multidisciplinary Digital Publishing Institute

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
2023-04 | Journal article | Author
DOI: 10.3390/ijms24097747
Contributors: Gennady Verkhivker; Mohammed Alshahrani; Grace Gupta; Sian Xiao; Peng Tao
Source: check_circle
Multidisciplinary Digital Publishing Institute

Mutational Scanning and Binding Free Energy Computations of the SARS-CoV-2 Spike Complexes with Distinct Groups of Neutralizing Antibodies: Energetic Drivers of Convergent Evolution of Binding Affinity and Immune Escape Hotspots
Source: check_circle
Multidisciplinary Digital Publishing Institute
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