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Gennady M. Verkhivker

University of California System

46H-index
256Paper Count
6.5KCitation Count
Published Papers 82
Publication Date
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Explainable AI reveals the allosteric blind spot in protein-ligand binding predictions
errCell Reports Physical Science
IF7.3
err2026-07-01
err0
PREAI
errParikh, Vedant; Foley, Brandon; Gatlin, Will; Ludwick, Max; Turano, Lucas; Verkhivker, Gennady M.
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Predicting and Decoding Allosteric Binding Sites Using Protein Language Models and Structure-Based Machine Learning: An Energy Landscape-Guided Explainable AI Framework
errJournal of Chemical Theory and Computation
IF5.5
err2026-05-06
err0
errOAAI
errKamila Riedlová; Vít Škrhák; William G. Gatlin; Max Ludwick; Lucas Turano; Marian Novotný; David Hoksza; Gennady M. Verkhivker
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Mechanisms of Binding and Immune Escape Resistance for Broadly Neutralizing Antibodies Targeting Distinct Conserved SARS-CoV-2 Spike Epitopes: A Hierarchical Approach Integrating Mutational Profiling and Energy Landscape Analysis
errInternational Journal of Molecular Sciences
IF4.9
err2026-04-30
err0
errOAAI
errMohammed Alshahrani; Will Gatlin; Max Ludwick; Lucas Turano; Brandon Foley; Gennady Verkhivker
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From Latent Manifolds to Targeted Molecular Probes: An Interpretable, Kinome-Scale Generative Machine Learning Framework for Family-Based Kinase Ligand Design
errBiomolecules
IF4.8
err2026-01-30
err0
errOAAI
errGennady Verkhivker; Ryan Kassab; Keerthi Krishnan
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Dissecting Binding and Immune Evasion Mechanisms for Ultrapotent Class I and Class 4/1 Neutralizing Antibodies of SARS-CoV-2 Spike Protein Using a Multi-Pronged Computational Approach: Neutral Frustration Architecture of Binding Interfaces and Immune Escape Hotspots Drives Adaptive Evolution
errphys. chem. chem. phys.
IF0
err2026-01-27
err0
PREAI
errMohammed Alshahrani; Vedant Parikh; Brandon Foley; Gennady M Verkhivker
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errSave
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
errBiomolecules 2025, Vol. 15, Page 1340
IF4.8
err2025-09-21
err0
errOAAI
errMohammed Alshahrani; Vedant Parikh; Brandon Foley; Gennady Verkhivker
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errSave
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
errViruses 2025, Vol. 17, Page 1029
IF3.5
err2025-08-22
err0
PREAI
errMohammed Alshahrani; Vedant Parikh; Brandon Foley; Gennady Verkhivker
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errSave
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
errPhys. Chem. Chem. Phys.
IF2.9
err2025-08-10
err0
PREAI
errMohammed Alshahrani; Vedant Parikh; Brandon Foley; Gennady M Verkhivker
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protPheMut: An Interpretable Machine Learning Tool for Classification of Cancer and Neurodevelopmental Disorders in Human Missense Mutations
errJournal of Chemical Information and Modeling
IF5.3
err2025-07-28
err0
PREAI
errJingran Wang; Miao Yang; Chang Zong; Yuan Li; Gennady Verkhivker; Fei Xiao; Guang Hu
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errSave
Exploring binding and allosteric energy landscapes for the KRAS interactions with effector proteins using Markov state modeling of conformational ensembles and allosteric network modeling
errProtein Science
IF5.2
err2025-07-16
err0
PREAI
errSian Xiao; Mohammed Alshahrani; Guang Hu; Peng Tao; Gennady Verkhivker
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errSave
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
errPHYSICAL CHEMISTRY CHEMICAL PHYSICS
IF2.9
err2025-01-01
err0
PREAI
errAlshahrani, Mohammed; Parikh, Vedant; Foley, Brandon; Hu, Guang; Verkhivker, Gennady
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errSave
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
errVIRUSES-BASEL
IF3.5
err2024-09-13
err8
errOAAI
errRaisinghani, Nishank; Alshahrani, Mohammed; Gupta, Grace; Verkhivker, Gennady
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errSave
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
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2024-06-12
err4
PREAI
errRaisinghani, Nishank; Alshahrani, Mohammed; Gupta, Grace; Tian, Hao; Xiao, Sian; Tao, Peng; Verkhivker, Gennady M.
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errSave
Accurate Characterization of Binding Kinetics and Allosteric Mechanisms for the HSP90 Chaperone Inhibitors Using AI-Augmented Integrative Biophysical Studies
errJACS AU
IF8.7
err2024-04-01
err3
errOAAI
errXu, Chao; Zhang, Xianglei; Zhao, Lianghao; Verkhivker, Gennady M.; Bai, Fang
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β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini
errJOURNAL OF COMPUTATIONAL CHEMISTRY
IF4.8
err2024-03-13
err1
errOAAI
errXiao, Sian; Ibrahim, Mayar Tarek; Verkhivker, Gennady M.; Zoltowski, Brian D.; Tao, Peng
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errSave
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
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2024-02-19
err2
PREAI
errRaisinghani, Nishank; Alshahrani, Mohammed; Gupta, Grace; Xiao, Sian; Tao, Peng; Verkhivker, Gennady
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errSave
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
errVIRUSES-BASEL
IF3.5
err2023-10-10
err5
errOAAI
errAlshahrani, Mohammed; Gupta, Grace; Xiao, Sian; Tao, Peng; Verkhivker, Gennady
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errSave
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
errVIRUSES-BASEL
IF3.5
err2023-09-27
err4
errOAAI
errVerkhivker, Gennady; Alshahrani, Mohammed; Gupta, Grace
errShare
errSave
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
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2023-08-07
err12
errOAAI
errXiao, Sian; Alshahrani, Mohammed; Gupta, Grace; Tao, Peng; Verkhivker, Gennady
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errSave
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
errVIRUSES-BASEL
IF3.5
err2023-05-10
err15
errOAAI
errVerkhivker, Gennady; Alshahrani, Mohammed; Gupta, Grace
errShare
errSave

Research Directions

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Co-authors
Cooperation Journals
N
Nicholas J. Schork
H-index: 138 · Papers: 785
D
Dario C. Altieri
H-index: 104 · Papers: 503
L
Len Neckers
H-index: 94 · Papers: 393
K
Karen L. Jones
H-index: 85 · Papers: 772
C
C. Russell Middaugh
H-index: 68 · Papers: 592
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