Docking Conformationally Flexible Small Molecules into a Protein Binding Site through Evolutionary Programming. - Daniel K. Gehlhaar; Gennady Verkhivker; Paul A. Rejto; David B. Fogel; Lawrence J. Fogel; Stephan T. Freer (Evolutionary Programming, 1995)

Thermodynamics and Kinetics of Ligand-Protein Binding Studied with the Weighted Histogram Analysis Method and Simulated Annealing. - 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 (Pacific Symposium on Biocomputing, 1999)

Deciphering common failures in molecular docking of ligand-protein complexes. - 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 (J. Comput. Aided Mol. Des., 2000)

Imprint of evolutionary conservation and protein structure variation on the binding function of protein tyrosine kinases. - Gennady Verkhivker (Bioinform., 2006)

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. - Gennady Verkhivker (WILF, 2007)

Exploring sequence-structure relationships in the tyrosine kinome space: functional classification of the binding specificity mechanisms for cancer therapeutics. - Gennady Verkhivker (Bioinform., 2007)

Coarse-Grained Modeling of the HIV-1 Protease Binding Mechanisms: I. Targeting Structural Flexibility of the Protease Flaps and Implications for Drug Design. - Gennady Verkhivker (CIBB, 2008)

Coarse-Grained Modeling of the HIV-1 Protease Binding Mechanisms: II. Folding Inhibition. - Gennady Verkhivker (CIBB, 2008)

Computational proteomics analysis of binding mechanisms and molecular signatures of the HIV-1 protease drugs. - Gennady Verkhivker (Artif. Intell. Medicine, 2009)

Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations. - Anshuman Dixit; Gennady Verkhivker (PLoS Comput. Biol., 2009)

Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer. - Giulia Morra; Gennady Verkhivker; Giorgio Colombo 001 (PLoS Comput. Biol., 2009)

Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases. - Anshuman Dixit; Gennady Verkhivker (PLoS Comput. Biol., 2011)

Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations. - Anshuman Dixit; Gennady Verkhivker (J. Chem. Inf. Model., 2012)

Experimentally Guided Structural Modeling and Dynamics Analysis of Hsp90-p53 Interactions: Allosteric Regulation of the Hsp90 Chaperone by a Client Protein. - Kristin Blacklock; Gennady Verkhivker (J. Chem. Inf. Model., 2013)

Structure-Functional Prediction and Analysis of Cancer Mutation Effects in Protein Kinases. - Anshuman Dixit; Gennady Verkhivker (Comput. Math. Methods Medicine, 2014)

Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications. - Kristin Blacklock; Gennady M. Verkhivker (PLoS Comput. Biol., 2014)

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. - Amanda Tse; Gennady M. Verkhivker (J. Chem. Inf. Model., 2015)

Integrating Genetic and Structural Data on Human Protein Kinome in Network-Based Modeling of Kinase Sensitivities and Resistance to Targeted and Personalized Anticancer Drugs. - Gennady M. Verkhivker (PSB, 2016)

Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks. - Gabrielle Stetz; Gennady M. Verkhivker (J. Chem. Inf. Model., 2016)

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication. - Gabrielle Stetz; Gennady M. Verkhivker (PLoS Comput. Biol., 2017)

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. - Steve Agajanian; Oluyemi Odeyemi; Nathaniel Bischoff; Simrath Ratra; Gennady M. Verkhivker (J. Chem. Inf. Model., 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. - Gabrielle Stetz; Gennady M. Verkhivker (J. Chem. Inf. Model., 2018)

Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis. - Hongyu Zhou; Zheng Dong; Gennady Verkhivker; Brian D. Zoltowski; Peng Tao 001 (PLoS Comput. Biol., 2019)

Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications. - Zhongjie Liang; Gennady M. Verkhivker; Guang Hu 001 (Briefings Bioinform., 2020)

Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 Mpro. - Olivier Sheik Amamuddy; Gennady M. Verkhivker; Özlem Tastan Bishop (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. - Lindy Astl; Gabrielle Stetz; Gennady M. Verkhivker (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. - Lindy Astl; Gennady M. Verkhivker (J. Chem. Inf. Model., 2020)

Comparative Dynamics and Functional Mechanisms of the CYP17A1 Tunnels Regulated by Ligand Binding. - Fei Xiao; Xingyu Song; Peiyi Tian; Mi Gan; Gennady M. Verkhivker; Guang Hu 001 (J. Chem. Inf. Model., 2020)

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. - Gennady M. Verkhivker; Steve Agajanian; Deniz Yasar Oztas; Grace Gupta (J. Chem. Inf. Model., 2021)

Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE. - Francesco Trozzi; Feng Wang 068; Gennady Verkhivker; Brian D. Zoltowski; Peng Tao 001 (PLoS Comput. Biol., 2021)

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. - Gennady M. Verkhivker; Steve Agajanian; Ryan Kassab; Keerthi Krishnan (J. Chem. Inf. Model., 2022)

Dissecting mutational allosteric effects in alkaline phosphatases associated with different Hypophosphatasia phenotypes: An integrative computational investigation. - Fei Xiao; Ziyun Zhou; Xingyu Song; Mi Gan; Jie Long; Gennady Verkhivker; Guang Hu 001 (PLoS Comput. Biol., 2022)

Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. - Steve Agajanian; Mohammed Alshahrani; Fang Bai; Peng Tao 001; Gennady M. Verkhivker (J. Chem. Inf. Model., 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. - Sian Xiao; Mohammed Alshahrani; Grace Gupta; Peng Tao 001; Gennady Verkhivker (J. Chem. Inf. Model., 2023)

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. - Nishank Raisinghani; Mohammed Alshahrani; Grace Gupta; Sian Xiao; Peng Tao 001; Gennady Verkhivker (J. Chem. Inf. Model., 2024)

β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. - Sian Xiao; Mayar Tarek Ibrahim; Gennady M. Verkhivker; Brian D. Zoltowski; Peng Tao 001 (J. Comput. Chem., 2024)

protPheMut: An Interpretable Machine Learning Tool for Classification of Cancer and Neurodevelopmental Disorders in Human Missense Mutations. - Jingran Wang; Miao Yang; Chang Zong; Yuan Li; Gennady Verkhivker; Fei Xiao; Guang Hu 001 (J. Chem. Inf. Model., 2025)

Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder. - Miao Yang; Jingran Wang; Ziyun Zhou; Wentian Li; Gennady Verkhivker; Fei Xiao; Guang Hu 001 (J. Chem. Inf. Model., 2025)