Gennady Verkhivker
Orcid: 0000-0002-4507-4471
According to our database1,
Gennady Verkhivker
authored at least 35 papers
between 1995 and 2024.
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Bibliography
2024
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.
J. Chem. Inf. Model., March, 2024
2023
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.
J. Chem. Inf. Model., August, 2023
Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches.
J. Chem. Inf. Model., March, 2023
2022
Dissecting mutational allosteric effects in alkaline phosphatases associated with different Hypophosphatasia phenotypes: An integrative computational investigation.
PLoS Comput. Biol., 2022
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.
J. Chem. Inf. Model., 2022
2021
PLoS Comput. Biol., 2021
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.
J. Chem. Inf. Model., 2021
2020
Comparative Dynamics and Functional Mechanisms of the CYP17A1 Tunnels Regulated by Ligand Binding.
J. Chem. Inf. Model., 2020
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.
J. Chem. Inf. Model., 2020
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.
J. Chem. Inf. Model., 2020
J. Chem. Inf. Model., 2020
Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications.
Briefings Bioinform., 2020
2019
Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis.
PLoS Comput. Biol., 2019
2018
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.
J. Chem. Inf. Model., 2018
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.
J. Chem. Inf. Model., 2018
2017
Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.
PLoS Comput. Biol., 2017
2016
Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks.
J. Chem. Inf. Model., 2016
Integrating Genetic and Structural Data on Human Protein Kinome in Network-Based Modeling of Kinase Sensitivities and Resistance to Targeted and Personalized Anticancer Drugs.
Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016
2015
Molecular Dynamics Simulations and Structural Network Analysis of c-Abl and c-Src Kinase Core Proteins: Capturing Allosteric Mechanisms and Communication Pathways from Residue Centrality.
J. Chem. Inf. Model., 2015
2014
Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications.
PLoS Comput. Biol., 2014
Structure-Functional Prediction and Analysis of Cancer Mutation Effects in Protein Kinases.
Comput. Math. Methods Medicine, 2014
2013
Experimentally Guided Structural Modeling and Dynamics Analysis of Hsp90-p53 Interactions: Allosteric Regulation of the Hsp90 Chaperone by a Client Protein.
J. Chem. Inf. Model., 2013
2012
Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations.
J. Chem. Inf. Model., 2012
2011
Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases.
PLoS Comput. Biol., 2011
2009
Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer.
PLoS Comput. Biol., 2009
Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations.
PLoS Comput. Biol., 2009
Computational proteomics analysis of binding mechanisms and molecular signatures of the HIV-1 protease drugs.
Artif. Intell. Medicine, 2009
2008
Coarse-Grained Modeling of the HIV-1 Protease Binding Mechanisms: II. Folding Inhibition.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2008
Coarse-Grained Modeling of the HIV-1 Protease Binding Mechanisms: I. Targeting Structural Flexibility of the Protease Flaps and Implications for Drug Design.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2008
2007
Exploring sequence-structure relationships in the tyrosine kinome space: functional classification of the binding specificity mechanisms for cancer therapeutics.
Bioinform., 2007
Computational Proteomics of Biomolecular Interactions in Sequence and Structure Space of the Tyrosine Kinome: Evolutionary Constraints and Protein Conformational Selection Determine Binding Signatures of Cancer Drugs.
Proceedings of the Applications of Fuzzy Sets Theory, 2007
2006
Imprint of evolutionary conservation and protein structure variation on the binding function of protein tyrosine kinases.
Bioinform., 2006
2000
J. Comput. Aided Mol. Des., 2000
1999
Thermodynamics and Kinetics of Ligand-Protein Binding Studied with the Weighted Histogram Analysis Method and Simulated Annealing.
Proceedings of the 4th Pacific Symposium on Biocomputing, 1999
1995
Docking Conformationally Flexible Small Molecules into a Protein Binding Site through Evolutionary Programming.
Proceedings of the Fourth Annual Conference on Evolutionary Programming, 1995