Gennady M. Verkhivker

15 papers Misc 1Journal 14

Year	Rank	Type	Title / Venue / Authors
2023	J	`jnl`	Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. J. Chem. Inf. Model. Steve Agajanian, Mohammed Alshahrani, Fang Bai, Peng Tao, Gennady M. Verkhivker
2022	J	`jnl`	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. Gennady M. Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan
2021	J	`jnl`	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. Gennady M. Verkhivker, Steve Agajanian, Deniz Yasar Oztas, Grace Gupta
2020	J	`jnl`	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. Lindy Astl, Gabrielle Stetz, Gennady M. Verkhivker
2020	J	`jnl`	Comparative Dynamics and Functional Mechanisms of the CYP17A1 Tunnels Regulated by Ligand Binding. J. Chem. Inf. Model. Fei Xiao, Xingyu Song, Peiyi Tian, Mi Gan, Gennady M. Verkhivker, Guang Hu
2020	J	`jnl`	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. Lindy Astl, Gennady M. Verkhivker
2020	J	`jnl`	Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 Mpro. J. Chem. Inf. Model. Olivier Sheik Amamuddy, Gennady M. Verkhivker, Özlem Tastan Bishop
2020	J	`jnl`	Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications. Briefings Bioinform. Zhongjie Liang, Gennady M. Verkhivker, Guang Hu
2018	J	`jnl`	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. Gabrielle Stetz, Gennady M. Verkhivker
2018	J	`jnl`	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. Steve Agajanian, Oluyemi Odeyemi, Nathaniel Bischoff, Simrath Ratra, Gennady M. Verkhivker
2017	J	`jnl`	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. Gabrielle Stetz, Gennady M. Verkhivker
2016	Misc	`conf`	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 Gennady M. Verkhivker
2016	J	`jnl`	Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks. J. Chem. Inf. Model. Gabrielle Stetz, Gennady M. Verkhivker
2015	J	`jnl`	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. Amanda Tse, Gennady M. Verkhivker
2014	J	`jnl`	Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications. PLoS Comput. Biol. Kristin Blacklock, Gennady M. Verkhivker