Gennady Verkhivker

Publication Activity (10 Years)

Years Active: 1995-2024
Publications (10 Years): 5

Top Topics

Machine Learning

Markov Property

Efficient Inference And Learning

Top Venues

PLoS Comput. Biol.

J. Chem. Inf. Model.

Comput. Math. Methods Medicine

Publications

Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady Verkhivker
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. 64 (5) (2024)
Sian Xiao, Mohammed Alshahrani, Grace Gupta, Peng Tao, Gennady Verkhivker
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. 63 (16) (2023)
Fei Xiao, Ziyun Zhou, Xingyu Song, Mi Gan, Jie Long, Gennady Verkhivker, Guang Hu
Dissecting mutational allosteric effects in alkaline phosphatases associated with different Hypophosphatasia phenotypes: An integrative computational investigation. PLoS Comput. Biol. 18 (3) (2022)
Francesco Trozzi, Feng Wang, Gennady Verkhivker, Brian D. Zoltowski, Peng Tao
Dimeric allostery mechanism of the plant circadian clock photoreceptor ZEITLUPE. PLoS Comput. Biol. 17 (7) (2021)
Hongyu Zhou, Zheng Dong, Gennady Verkhivker, Brian D. Zoltowski, Peng Tao
Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis. PLoS Comput. Biol. 15 (2) (2019)
Anshuman Dixit, Gennady Verkhivker
Structure-Functional Prediction and Analysis of Cancer Mutation Effects in Protein Kinases. Comput. Math. Methods Medicine 2014 (2014)
Kristin Blacklock, Gennady Verkhivker
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. 53 (11) (2013)
Anshuman Dixit, Gennady Verkhivker
Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations. J. Chem. Inf. Model. 52 (10) (2012)
Anshuman Dixit, Gennady Verkhivker
Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases. PLoS Comput. Biol. 7 (10) (2011)
Giulia Morra, Gennady Verkhivker, Giorgio Colombo
Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer. PLoS Comput. Biol. 5 (3) (2009)
Gennady Verkhivker
Computational proteomics analysis of binding mechanisms and molecular signatures of the HIV-1 protease drugs. Artif. Intell. Medicine 45 (2-3) (2009)
Anshuman Dixit, Gennady Verkhivker
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. 5 (8) (2009)
Gennady Verkhivker
Coarse-Grained Modeling of the HIV-1 Protease Binding Mechanisms: I. Targeting Structural Flexibility of the Protease Flaps and Implications for Drug Design. CIBB (2008)
Gennady Verkhivker
Coarse-Grained Modeling of the HIV-1 Protease Binding Mechanisms: II. Folding Inhibition. CIBB (2008)
Gennady Verkhivker
Exploring sequence-structure relationships in the tyrosine kinome space: functional classification of the binding specificity mechanisms for cancer therapeutics. Bioinform. 23 (15) (2007)
Gennady Verkhivker
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 (2007)
Gennady Verkhivker
Imprint of evolutionary conservation and protein structure variation on the binding function of protein tyrosine kinases. Bioinform. 22 (15) (2006)
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
Deciphering common failures in molecular docking of ligand-protein complexes. J. Comput. Aided Mol. Des. 14 (8) (2000)
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
Thermodynamics and Kinetics of Ligand-Protein Binding Studied with the Weighted Histogram Analysis Method and Simulated Annealing. Pacific Symposium on Biocomputing (1999)
Daniel K. Gehlhaar, Gennady Verkhivker, Paul A. Rejto, David B. Fogel, Lawrence J. Fogel, Stephan T. Freer
Docking Conformationally Flexible Small Molecules into a Protein Binding Site through Evolutionary Programming. Evolutionary Programming (1995)