Publications by authors named "Vedant Parikh"

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Neutral Frustration Landscape Architecture of SARS-CoV-2 Spike-Antibody Interfaces Shapes Immune Evasion Mechanisms for Ultrapotent Neutralizing Antibodies and Determines Pathways of Viral Adaptation: Insights from Integrative Computational Approach.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady Verkhivker

bioRxiv· November 2025

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Dynamic mutational profiling of binding interactions and allosteric networks in conformational ensembles of the SARS-CoV-2 spike protein complexes with classes of antibodies targeting cryptic binding sites: confluence of binding and allostery determines molecular mechanisms and hotspots of immune escape.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady Verkhivker

Phys Chem Chem Phys· September 2025

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Allosteric Control Overcomes Steric Limitations for Neutralizing Antibodies Targeting Conserved Binding Epitopes of the SARS-CoV-2 Spike Protein: Exploring the Intersection of Binding, Allostery, and Immune Escape with a Multimodal Computational Approach.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady Verkhivker

Biomolecules· September 2025

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Exploring Dynamic Modulation of Binding, Allostery and Immune Resistance in the SARS-CoV-2 Spike Complexes with Classes of Antibodies Targeting Cryptic Binding Sites: Antibody-Specific Augmentations of Conserved Allosteric Architecture Can Influence Evolution of Viral Escape.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady Verkhivker

bioRxiv· July 2025

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Deciphering the Mechanistic Continuum of Broadly Neutralizing Class 4 Antibodies Targeting Conserved Cryptic Epitopes of the SARS-CoV-2 Spike Protein : Operating at the Intersection of Binding, Allostery and Immune Escape.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady Verkhivker

bioRxiv· July 2025

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Multiscale Modeling and Dynamic Mutational Profiling of Binding Energetics and Immune Escape for Class I Antibodies with SARS-CoV-2 Spike Protein: Dissecting Mechanisms of High Resistance to Viral Escape Against Emerging Variants.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady Verkhivker

Viruses· July 2025

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Conformational Landscaping and Dynamic Mutational Profiling of Binding Interactions and Immune Escape for Broadly Neutralizing Class I Antibodies with SARS-CoV-2 Spike Protein: Distributed Binding Hotspot Networks Underlie Mechanism of Viral Resistance Against Existing Variants.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady Verkhivker

bioRxiv· June 2025

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Ensemble-Based Binding Free Energy Profiling and Network Analysis of the KRAS Interactions with DARPin Proteins Targeting Distinct Binding Sites: Revealing Molecular Determinants and Universal Architecture of Regulatory Hotspots and Allosteric Binding.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady Verkhivker

Biomolecules· June 2025

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Probing binding and allosteric mechanisms of the KRAS interactions with monobodies and affimer proteins: ensemble-based mutational profiling and thermodynamic analysis of binding energetics and allostery reveal diversity of functional hotspots and cryptic pockets linked by conserved communication network.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Guang Hu, Gennady Verkhivker

Phys Chem Chem Phys· May 2025

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A Conserved Architecture of Allosteric Communications and Regulatory Hotspots in the KRAS Complexes with Diverse Binding Proteins Controls Mechanisms of Effector Mimicry and Allosteric Modulation : Atomistic Revelations from Molecular Simulations and Mutational Scanning of Binding Energetics and Allostery.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady Verkhivker

bioRxiv· May 2025

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Integrative Computational Modeling of Distinct Binding Mechanisms for Broadly Neutralizing Antibodies Targeting SARS-CoV-2 Spike Omicron Variants: Balance of Evolutionary and Dynamic Adaptability in Shaping Molecular Determinants of Immune Escape.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady Verkhivker

Viruses· May 2025

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Exploring Diverse Binding Mechanisms of Broadly Neutralizing Antibodies S309, S304, CYFN-1006 and VIR-7229 Targeting SARS-CoV-2 Spike Omicron Variants: Integrative Computational Modeling Reveals Balance of Evolutionary and Dynamic Adaptability in Shaping Molecular Determinants of Immune Escape.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady Verkhivker

bioRxiv· April 2025

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Atomistic Profiling of KRAS Interactions with Monobodies and Affimer Proteins Through Ensemble-Based Mutational Scanning Unveils Conserved Residue Networks Linking Cryptic Pockets and Regulating Mechanisms of Binding, Specificity and Allostery.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Guang Hu, Gennady Verkhivker

bioRxiv· March 2025

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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.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady Verkhivker

Biomolecules· February 2025

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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.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady Verkhivker

Int J Mol Sci· February 2025

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AlphaFold2-Based Characterization of Apo and Holo Protein Structures and Conformational Ensembles Using Randomized Alanine Sequence Scanning Adaptation: Capturing Shared Signature Dynamics and Ligand-Induced Conformational Changes.
Nishank Raisinghani, Vedant Parikh, Brandon Foley, Gennady Verkhivker

Int J Mol Sci· December 2024

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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.
Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady Verkhivker

bioRxiv· December 2024

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Assessing Structures and Conformational Ensembles of Apo and Holo Protein States Using Randomized Alanine Sequence Scanning Combined with Shallow Subsampling in AlphaFold2 : Insights and Lessons from Predictions of Functional Allosteric Conformations.
Nishank Raisinghani, Vedant Parikh, Brandon Foley, Gennady Verkhivker

bioRxiv· November 2024

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Comparative Analysis of Fusion Strategies for Imaging and Non-imaging Data - Use-case of Hospital Discharge Prediction.
Vedant Parikh, Amara Tariq, Bhavik Patel, Imon Banerjee

AMIA Jt Summits Transl Sci Proc· May 2024

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