Gennady M. Verkhivker

Also affiliated with University of California San Diego, University of Montana

MedicineBiochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

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Indexed papers

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datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 47 papers. Top paper: “Integrated Computational Approaches and Tools for Allosteric Drug Discovery”.

Integrated Computational Approaches and Tools for Allosteric Drug Discovery

International Journal of Molecular Sciences(2020)10.3390/ijms21030847

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108 citations

Wayde Veldman, Colleen Varaidzo Manyumwa, Afrah Khairallah, Steve Agajanian, Oluyemi Odeyemi +3 more

Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE

PLoS Computational Biology(2021)10.1371/journal.pcbi.1009168

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6 citations

Feng Wang, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao, Francesco Trozzi

Machine learning and protein allostery

Trends in Biochemical Sciences(2022)10.1016/j.tibs.2022.12.001

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33 citations

Gennady M. Verkhivker, Peng Tao, Sian Xiao

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)10.1021/acs.jcim.3c00778

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43 citations

Mohammed Alshahrani, Grace Gupta, Peng Tao, Gennady M. Verkhivker, Sian Xiao

Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.2c01634

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37 citations

Mohammed Alshahrani, Fang Bai, Peng Tao, Gennady M. Verkhivker, Steve Agajanian

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(2023)10.1039/d3cp02042h

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16 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker

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)10.3390/ijms24097747

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15 citations

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(2023)10.3390/v15102073

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9 citations

Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker, Mohammed Alshahrani

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 (Cold Spring Harbor Laboratory)(2023)10.1101/2023.09.11.557205

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Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker, Mohammed Alshahrani

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 (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.03.539337

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0 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, 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 (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.20.541592

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0 citations

Mohammed Alshahrani, Grace Gupta, Peng Tao, Gennady M. Verkhivker, Sian Xiao

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 (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.18.567697

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Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

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 (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.11.571185

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0 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

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

鐵と鋼 : 日本鐡鋼協會々誌(2023)10.1101/2023.12.22.573121

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Mayar Tarek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao, Sian Xiao

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)10.3390/v16091458

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28 citations

Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker, Nishank Raisinghani

Accurate Characterization of Binding Kinetics and Allosteric Mechanisms for the HSP90 Chaperone Inhibitors Using AI-Augmented Integrative Biophysical Studies

JACS Au(2024)10.1021/jacsau.4c00123

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18 citations

Xianglei Zhang, Lianghao Zhao, Gennady M. Verkhivker, Fang Bai, Chao Xu

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)10.1021/acs.jctc.4c00222

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17 citations

Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao +2 more

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)10.1021/acs.jpcb.4c01341

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17 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

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)10.3390/ijms25084281

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16 citations

Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker, Nishank Raisinghani

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(2024)10.1039/d4cp01372g

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13 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

Exploring Binding Pockets in the Conformational States of the SARS-CoV-2 Spike Trimers for the Screening of Allosteric Inhibitors Using Molecular Simulations and Ensemble-Based Ligand Docking

International Journal of Molecular Sciences(2024)10.3390/ijms25094955

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6 citations

Gennady M. Verkhivker, Grace Gupta

β‐sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini

Journal of Computational Chemistry(2024)10.1002/jcc.27344

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5 citations

Mayar Tarek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao, Sian Xiao

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)10.1021/acs.jcim.3c01857

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7 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

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)10.3390/ijms251810082

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6 citations

Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker, Nishank Raisinghani

Probing Functional Allosteric States and Conformational Ensembles of the Allosteric Protein Kinase States and Mutants: Atomistic Modeling and Comparative Analysis of AlphaFold2, OmegaFold, and AlphaFlow Approaches and Adaptations

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c04985

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5 citations

Mohammed Merae Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao +2 more

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 (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.02.587850

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7 citations

Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker +1 more

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 (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.15.580591

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5 citations

Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao +2 more

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)10.3390/biom15020249

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9 citations

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

Exploring binding and allosteric energy landscapes for the KRAS interactions with effector proteins using Markov state modeling of conformational ensembles and allosteric network modeling

Protein Science(2025)10.1002/pro.70228

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9 citations

Mohammed Merae Alshahrani, Guang Hu, Peng Tao, Gennady M. Verkhivker, Sian Xiao

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

Viruses(2025)10.3390/v17060741

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6 citations

Vedant Parikh, Brandon Foley, Gennady M. Verkhivker, Mohammed Alshahrani

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

Viruses(2025)10.3390/v17081029

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3 citations

Vedant Parikh, Brandon Foley, Gennady M. Verkhivker, Mohammed Alshahrani

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

Physical Chemistry Chemical Physics(2025)10.1039/d5cp02468d

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3 citations

Vedant Parikh, Brandon Foley, Gennady M. Verkhivker, Mohammed Alshahrani

protPheMut: An Interpretable Machine Learning Tool for Classification of Cancer and Neurodevelopmental Disorders in Human Missense Mutations

Journal of Chemical Information and Modeling(2025)10.1021/acs.jcim.5c01219

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1 citations

Miao Yang, Chang Zong, Yuan Li, Gennady M. Verkhivker, Fei Xiao +2 more

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

Biomolecules(2025)10.3390/biom15091340

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1 citations

Vedant Parikh, Brandon Foley, Gennady M. Verkhivker, Mohammed Alshahrani

Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder

Journal of Chemical Information and Modeling(2025)10.1021/acs.jcim.5c00134

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2 citations

Jingran Wang, Ziyun Zhou, Wentian Li, Gennady M. Verkhivker, Fei Xiao +2 more

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)10.3390/ijms26041507

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1 citations

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

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

Preprints.org(2025)10.20944/preprints202501.0507.v1

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2 citations

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

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

Preprints.org(2025)10.20944/preprints202504.1325.v1

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2 citations

Vedant Parikh, Brandon Foley, Gennady M. Verkhivker, Mohammed Alshahrani

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

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.31.685956

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2 citations

Vedant Parikh, Brandon Foley, Gennady M. Verkhivker, Mohammed Alshahrani

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

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.05.19.654934

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1 citations

Vedant Parikh, Brandon Foley, Gennady M. Verkhivker, Mohammed Alshahrani

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

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.03.11.642708

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Vedant Parikh, Brandon Foley, Guang Hu, Gennady M. Verkhivker, Mohammed Alshahrani

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

Biomolecules(2025)10.3390/biom15060819

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Vedant Parikh, Brandon Foley, Gennady M. Verkhivker, Mohammed Alshahrani

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

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.06.07.658468

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Vedant Parikh, Brandon Foley, Gennady M. Verkhivker, Mohammed Alshahrani

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

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.06.28.662162

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Vedant Parikh, Brandon Foley, Gennady M. Verkhivker, Mohammed Alshahrani

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

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.10.664240

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0 citations

Vedant Parikh, Brandon Foley, Gennady M. Verkhivker, Mohammed Alshahrani

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 Multimodal Computational Approach

Preprints.org(2025)10.20944/preprints202507.1050.v1

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Vedant Parikh, Brandon Foley, Gennady M. Verkhivker, Mohammed Alshahrani

From Latent Manifolds to Functional Probes: An Interpretable, Kinome-Scale Generative Machine Learning Framework for Family-Targeted Kinase Inhibitor Design

Preprints.org(2025)10.20944/preprints202511.1117.v1

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Ryan Kassab, Keerthi Krishnan, Gennady M. Verkhivker