Gennady M. Verkhivker

Publication Activity (10 Years)

Years Active: 2014-2024
Publications (10 Years): 14

Top Topics

High Throughput

Molecular Dynamics

Protein Complexes

Computational Modeling

Top Venues

J. Chem. Inf. Model.

PLoS Comput. Biol.

Briefings Bioinform.

J. Comput. Chem.

Publications

Sian Xiao, Mayar Tarek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao
LOV2 termini. J. Comput. Chem. 45 (17) (2024)
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. J. Chem. Inf. Model. 63 (5) (2023)
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. J. Chem. Inf. Model. 62 (8) (2022)
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. J. Chem. Inf. Model. 61 (10) (2021)
Olivier Sheik Amamuddy, Gennady M. Verkhivker, Özlem Tastan Bishop
Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 Mpro. J. Chem. Inf. Model. 60 (10) (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. J. Chem. Inf. Model. 60 (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. J. Chem. Inf. Model. 60 (7) (2020)
Zhongjie Liang, Gennady M. Verkhivker, Guang Hu
Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications. Briefings Bioinform. 21 (3) (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. J. Chem. Inf. Model. 60 (3) (2020)
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. J. Chem. Inf. Model. 58 (2) (2018)
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. J. Chem. Inf. Model. 58 (10) (2018)
Gabrielle Stetz, Gennady M. Verkhivker
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. 13 (1) (2017)
Gennady M. Verkhivker
Integrating Genetic and Structural Data on Human Protein Kinome in Network-Based Modeling of Kinase Sensitivities and Resistance to Targeted and Personalized Anticancer Drugs. PSB (2016)
Gabrielle Stetz, Gennady M. Verkhivker
Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks. J. Chem. Inf. Model. 56 (8) (2016)
Amanda Tse, Gennady M. Verkhivker
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. 55 (8) (2015)
Kristin Blacklock, Gennady M. Verkhivker
Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications. PLoS Comput. Biol. 10 (6) (2014)