Gennady Verkhivker

23 papers Misc 1Journal 17Unranked 4

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder. J. Chem. Inf. Model. Miao Yang, Jingran Wang, Ziyun Zhou, Wentian Li, Gennady Verkhivker, Fei Xiao, Guang Hu
2025	J	`jnl`	protPheMut: An Interpretable Machine Learning Tool for Classification of Cancer and Neurodevelopmental Disorders in Human Missense Mutations. J. Chem. Inf. Model. Jingran Wang, Miao Yang, Chang Zong, Yuan Li, Gennady Verkhivker, Fei Xiao, Guang Hu
2024	J	`jnl`	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. Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady Verkhivker
2023	J	`jnl`	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. Sian Xiao, Mohammed Alshahrani, Grace Gupta, Peng Tao, Gennady Verkhivker
2022	J	`jnl`	Dissecting mutational allosteric effects in alkaline phosphatases associated with different Hypophosphatasia phenotypes: An integrative computational investigation. PLoS Comput. Biol. Fei Xiao, Ziyun Zhou, Xingyu Song, Mi Gan, Jie Long, Gennady Verkhivker, Guang Hu
2021	J	`jnl`	Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE. PLoS Comput. Biol. Francesco Trozzi, Feng Wang, Gennady Verkhivker, Brian D. Zoltowski, Peng Tao
2019	J	`jnl`	Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis. PLoS Comput. Biol. Hongyu Zhou, Zheng Dong, Gennady Verkhivker, Brian D. Zoltowski, Peng Tao
2014	J	`jnl`	Structure-Functional Prediction and Analysis of Cancer Mutation Effects in Protein Kinases. Comput. Math. Methods Medicine Anshuman Dixit, Gennady Verkhivker
2013	J	`jnl`	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. Kristin Blacklock, Gennady Verkhivker
2012	J	`jnl`	Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations. J. Chem. Inf. Model. Anshuman Dixit, Gennady Verkhivker
2011	J	`jnl`	Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases. PLoS Comput. Biol. Anshuman Dixit, Gennady Verkhivker
2009	—	`ed.`	Computational Intelligence Methods for Bioinformatics and Biostatistics, 5th International Meeting, CIBB 2008, Vietri sul Mare, Italy, October 3-4, 2008, Revised Selected Papers CIBB Francesco Masulli, Roberto Tagliaferri, Gennady Verkhivker
2009	J	`jnl`	Computational proteomics analysis of binding mechanisms and molecular signatures of the HIV-1 protease drugs. Artif. Intell. Medicine Gennady Verkhivker
2009	J	`jnl`	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. Anshuman Dixit, Gennady Verkhivker
2009	J	`jnl`	Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer. PLoS Comput. Biol. Giulia Morra, Gennady Verkhivker, Giorgio Colombo
2008	—	`conf`	Coarse-Grained Modeling of the HIV-1 Protease Binding Mechanisms: I. Targeting Structural Flexibility of the Protease Flaps and Implications for Drug Design. CIBB Gennady Verkhivker
2008	—	`conf`	Coarse-Grained Modeling of the HIV-1 Protease Binding Mechanisms: II. Folding Inhibition. CIBB Gennady Verkhivker
2007	—	`conf`	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. WILF Gennady Verkhivker
2007	J	`jnl`	Exploring sequence-structure relationships in the tyrosine kinome space: functional classification of the binding specificity mechanisms for cancer therapeutics. Bioinform. Gennady Verkhivker
2006	J	`jnl`	Imprint of evolutionary conservation and protein structure variation on the binding function of protein tyrosine kinases. Bioinform. Gennady Verkhivker
2000	J	`jnl`	Deciphering common failures in molecular docking of ligand-protein complexes. J. Comput. Aided Mol. Des. Gennady Verkhivker, Djamal Bouzida, Daniel K. Gehlhaar, Paul A. Rejto, Sandra Arthurs, Anthony B. Colson, Stephan T. Freer, Veda Larson, Brock A. Luty, Tami Marrone, Peter W. Rose
1999	Misc	`conf`	Thermodynamics and Kinetics of Ligand-Protein Binding Studied with the Weighted Histogram Analysis Method and Simulated Annealing. Pacific Symposium on Biocomputing Djamal Bouzida, Sandra Arthurs, Anthony B. Colson, Stephan T. Freer, Daniel K. Gehlhaar, Veda Larson, Brock A. Luty, Paul A. Rejto, Peter W. Rose, Gennady Verkhivker
1995	—	`conf`	Docking Conformationally Flexible Small Molecules into a Protein Binding Site through Evolutionary Programming. Evolutionary Programming Daniel K. Gehlhaar, Gennady Verkhivker, Paul A. Rejto, David B. Fogel, Lawrence J. Fogel, Stephan T. Freer