Gennady M Verkhivker (Gennady Verkhivker)

Loop profile ResearcherID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 89

Top Topics

Machine Learning

Molecular Dynamics

Top Venues

International journal of molecular sciences

Journal of chemical information and modeling

bioRxiv : the preprint server for biology

Journal of chemical theory and computation

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, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
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 20 (12) (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)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. Journal of computational chemistry (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
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 64 (5) (2024)
Grace Gupta, Gennady M Verkhivker
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 25 (9) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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 64 (5) (2024)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. Journal of computational chemistry 45 (17) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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 128 (19) (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
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 128 (19) (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)
Chao Xu, Xianglei Zhang, Lianghao Zhao, Gennady M Verkhivker, Fang Bai
Accurate Characterization of Binding Kinetics and Allosteric Mechanisms for the HSP90 Chaperone Inhibitors Using AI-Augmented Integrative Biophysical Studies. JACS Au 4 (4) (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
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)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. Journal of computational chemistry 45 (17) (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
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)
Grace Gupta, Gennady M Verkhivker
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 25 (9) (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Gennady M Verkhivker
Atomistic Prediction of Structures, Conformational Ensembles and Binding Energetics for the SARS-CoV-2 Spike JN.1, KP.2 and KP.3 Variants Using AlphaFold2 and Molecular Dynamics Simulations: Mutational Profiling and Binding Free Energy Analysis Reveal Epistatic Hotspots of the ACE2 Affinity and Immune Escape. bioRxiv : the preprint server for biology (2024)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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 64 (5) (2024)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. Journal of computational chemistry 45 (17) (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
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)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Hao Tian, Sian Xiao, Peng Tao, Gennady M Verkhivker
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 20 (12) (2024)
Chao Xu, Xianglei Zhang, Lianghao Zhao, Gennady M Verkhivker, Fang Bai
Accurate Characterization of Binding Kinetics and Allosteric Mechanisms for the HSP90 Chaperone Inhibitors Using AI-Augmented Integrative Biophysical Studies. JACS Au 4 (4) (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)
Keerthi Krishnan, Hao Tian, Peng Tao, Gennady M Verkhivker
Probing conformational landscapes and mechanisms of allosteric communication in the functional states of the ABL kinase domain using multiscale simulations and network-based mutational profiling of allosteric residue potentials. The Journal of chemical physics 157 (24) (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 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)
Sian Xiao, Mayar Tarek Ibrahim, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
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. bioRxiv : the preprint server for biology (2023)
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)
Mayar Tarek Ibrahim, Gennady M Verkhivker, Jyoti Misra, Peng Tao
Novel Allosteric Effectors Targeting Human Transcription Factor TEAD. International journal of molecular sciences 24 (10) (2023)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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 : the preprint server for biology (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. bioRxiv : the preprint server for biology (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)
Steve Agajanian, Mohammed Alshahrani, Fang Bai, Peng Tao, Gennady M Verkhivker
Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. Journal of chemical information and modeling 63 (5) (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. bioRxiv : the preprint server for biology (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)
Steve Agajanian, Mohammed Alshahrani, Fang Bai, Peng Tao, Gennady M Verkhivker
Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. Journal of chemical information and modeling 63 (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)
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)
Steve Agajanian, Mohammed Alshahrani, Fang Bai, Peng Tao, Gennady M Verkhivker
Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. Journal of chemical information and modeling (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)
Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M Verkhivker
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 : the preprint server for biology (2023)
Gennady M Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan
Frustration-driven allosteric regulation and signal transmission in the SARS-CoV-2 spike omicron trimer structures: a crosstalk of the omicron mutation sites allosterically regulates tradeoffs of protein stability and conformational adaptability. Physical chemistry chemical physics : PCCP 24 (29) (2022)
Gennady M Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan
Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations. International journal of molecular sciences 23 (8) (2022)
Gennady M Verkhivker
Conformational Dynamics and Mechanisms of Client Protein Integration into the Hsp90 Chaperone Controlled by Allosteric Interactions of Regulatory Switches: Perturbation-Based Network Approach for Mutational Profiling of the Hsp90 Binding and Allostery. The journal of physical chemistry. B (2022)
Gennady M Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan
Probing Mechanisms of Binding and Allostery in the SARS-CoV-2 Spike Omicron Variant Complexes with the Host Receptor: Revealing Functional Roles of the Binding Hotspots in Mediating Epistatic Effects and Communication with Allosteric Pockets. International journal of molecular sciences 23 (19) (2022)
Gennady M Verkhivker
Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering. International journal of molecular sciences 23 (6) (2022)
Gennady M Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan
Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike Variants. Journal of chemical information and modeling 62 (8) (2022)
Keerthi Krishnan, Ryan Kassab, Steve Agajanian, Gennady M Verkhivker
Interpretable Machine Learning Models for Molecular Design of Tyrosine Kinase Inhibitors Using Variational Autoencoders and Perturbation-Based Approach of Chemical Space Exploration. International journal of molecular sciences 23 (19) (2022)
Gennady M Verkhivker
Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant. International journal of molecular sciences 23 (4) (2022)
Gennady M Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan
Integrating Conformational Dynamics and Perturbation-Based Network Modeling for Mutational Profiling of Binding and Allostery in the SARS-CoV-2 Spike Variant Complexes with Antibodies: Balancing Local and Global Determinants of Mutational Escape Mechanisms. Biomolecules 12 (7) (2022)
Hamid Hadi-Alijanvand, Luisa Di Paola, Guang Hu, David M Leitner, Gennady M Verkhivker, Peixin Sun, Humanath Poudel, Alessandro Giuliani
Biophysical Insight into the SARS-CoV2 Spike-ACE2 Interaction and Its Modulation by Hepcidin through a Multifaceted Computational Approach. ACS omega 7 (20) (2022)
Gennady M Verkhivker
Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability. International journal of molecular sciences 23 (3) (2022)
Gennady M Verkhivker, Steve Agajanian, Deniz Yasar Oztas, Grace Gupta
Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. ACS omega 6 (24) (2021)
Gennady M Verkhivker, Steve Agajanian, Deniz Yasar Oztas, Grace Gupta
Atomistic Simulations and In Silico Mutational Profiling of Protein Stability and Binding in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Molecular Determinants of Mutational Escape Mechanisms. ACS omega 6 (40) (2021)
Gennady M Verkhivker, Steve Agajanian, Deniz Yasar Oztas, Grace Gupta
Allosteric Control of Structural Mimicry and Mutational Escape in the SARS-CoV-2 Spike Protein Complexes with the ACE2 Decoys and Miniprotein Inhibitors: A Network-Based Approach for Mutational Profiling of Binding and Signaling. Journal of chemical information and modeling 61 (10) (2021)
Gennady M Verkhivker, Luisa Di Paola
Dynamic Network Modeling of Allosteric Interactions and Communication Pathways in the SARS-CoV-2 Spike Trimer Mutants: Differential Modulation of Conformational Landscapes and Signal Transmission via Cascades of Regulatory Switches. The journal of physical chemistry. B 125 (3) (2021)
Gennady M Verkhivker, Luisa Di Paola
Integrated Biophysical Modeling of the SARS-CoV-2 Spike Protein Binding and Allosteric Interactions with Antibodies. The journal of physical chemistry. B 125 (18) (2021)
Gennady M Verkhivker, Steve Agajanian, Deniz Yazar Oztas, Grace Gupta
Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies: Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations. Biochemistry 60 (19) (2021)
Francesco Trozzi, Feng Wang, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE. PLoS computational biology 17 (7) (2021)
Gennady M Verkhivker, Steve Agajanian, Deniz Oztas, Grace Gupta
Dynamic Profiling of Binding and Allosteric Propensities of the SARS-CoV-2 Spike Protein with Different Classes of Antibodies: Mutational and Perturbation-Based Scanning Reveals the Allosteric Duality of Functionally Adaptable Hotspots. Journal of chemical theory and computation 17 (7) (2021)
Lindy Astl, Gabrielle Stetz, Gennady M Verkhivker
Dissecting Molecular Principles of the Hsp90 Chaperone Regulation by Allosteric Modulators Using a Hierarchical Simulation Approach and Network Modeling of Allosteric Interactions: Conformational Selection Dictates the Diversity of Protein Responses and Ligand-Specific Functional Mechanisms. Journal of chemical theory and computation 16 (10) (2020)
Olivier Sheik Amamuddy, Wayde Veldman, Colleen Varaidzo Manyumwa, Afrah Khairallah, Steve Agajanian, Odeyemi Oluyemi, Gennady M Verkhivker, Ozlem Tastan Bishop
Integrated Computational Approaches and Tools forAllosteric Drug Discovery. International journal of molecular sciences 21 (3) (2020)
Lindy Astl, Gabrielle Stetz, Gennady M Verkhivker
Allosteric Mechanism of the Hsp90 Chaperone Interactions with Cochaperones and Client Proteins by Modulating Communication Spines of Coupled Regulatory Switches: Integrative Atomistic Modeling of Hsp90 Signaling in Dynamic Interaction Networks. Journal of chemical information and modeling 60 (7) (2020)
Lindy Astl, Gennady M Verkhivker
Dynamic View of Allosteric Regulation in the Hsp70 Chaperones by J-Domain Cochaperone and Post-Translational Modifications: Computational Analysis of Hsp70 Mechanisms by Exploring Conformational Landscapes and Residue Interaction Networks. Journal of chemical information and modeling 60 (3) (2020)
Gennady M Verkhivker
Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike Proteins. Journal of proteome research 19 (11) (2020)
Olivier Sheik Amamuddy, Gennady M Verkhivker, Ozlem Tastan Bishop
Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 Mpro. Journal of chemical information and modeling 60 (10) (2020)
Gabrielle Stetz, Lindy Astl, Gennady M Verkhivker
Exploring Mechanisms of Communication Switching in the Hsp90-Cdc37 Regulatory Complexes with Client Kinases through Allosteric Coupling of Phosphorylation Sites: Perturbation-Based Modeling and Hierarchical Community Analysis of Residue Interaction Networks. Journal of chemical theory and computation 16 (7) (2020)
Fei Xiao, Xingyu Song, Peiyi Tian, Mi Gan, Gennady M Verkhivker, Guang Hu
Comparative Dynamics and Functional Mechanisms of the CYP17A1 Tunnels Regulated by Ligand Binding. Journal of chemical information and modeling 60 (7) (2020)
Gennady M Verkhivker
Coevolution, Dynamics and Allostery Conspire in Shaping Cooperative Binding and Signal Transmission of the SARS-CoV-2 Spike Protein with Human Angiotensin-Converting Enzyme 2. International journal of molecular sciences 21 (21) (2020)
Hongyu Zhou, Zheng Dong, Gennady M Verkhivker, Brian D Zoltowski, Peng Tao
Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis. PLoS computational biology 15 (2) (2019)
Lindy Astl, Gennady M Verkhivker
Atomistic Modeling of the ABL Kinase Regulation by Allosteric Modulators Using Structural Perturbation Analysis and Community-Based Network Reconstruction of Allosteric Communications. Journal of chemical theory and computation 15 (5) (2019)
Steve Agajanian, Oluyemi Odeyemi, Nathaniel Bischoff, Simrath Ratra, Gennady M Verkhivker
Machine Learning Classification and Structure-Functional Analysis of Cancer Mutations Reveal Unique Dynamic and Network Signatures of Driver Sites in Oncogenes and Tumor Suppressor Genes. Journal of chemical information and modeling 58 (10) (2018)
Gabrielle Stetz, Gennady M Verkhivker
Functional Role and Hierarchy of the Intermolecular Interactions in Binding of Protein Kinase Clients to the Hsp90-Cdc37 Chaperone: Structure-Based Network Modeling of Allosteric Regulation. Journal of chemical information and modeling 58 (2) (2018)
Gabrielle Stetz, Amanda Tse, Gennady M Verkhivker
Dissecting Structure-Encoded Determinants of Allosteric Cross-Talk between Post-Translational Modification Sites in the Hsp90 Chaperones. Scientific reports 8 (1) (2018)
Josh Czemeres, Kurt Buse, Gennady M Verkhivker
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