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ORCIDGennady Verkhivker
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Journal Articles
- 2024
[j30]Sian Xiao
, Mayar Tarek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao:
β-sheets mediate the conformational change and allosteric signal transmission between the AsLOV2 termini. J. Comput. Chem. 45(17): 1493-1504 (2024)- [j29]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): 1657-1681 (2024) - 2023
- [j28]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): 1413-1428 (2023) - [j27]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): 5272-5296 (2023) - 2022
- [j26]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): 1956-1978 (2022) - [j25]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) - 2021
- [j24]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): 5172-5191 (2021) - [j23]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) - 2020
- [j22]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): 815-835 (2020) - [j21]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): 1614-1631 (2020) - [j20]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): 3616-3631 (2020) - [j19]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): 3632-3647 (2020) - [j18]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): 5080-5102 (2020) - 2019
- [j17]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) - 2018
- [j16]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): 405-421 (2018) - [j15]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): 2131-2150 (2018) - 2017
- [j14]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) - 2016
- [j13]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): 1490-1517 (2016) - 2015
- [j12]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): 1645-1662 (2015) - 2014
- [j11]Anshuman Dixit, Gennady Verkhivker:
Structure-Functional Prediction and Analysis of Cancer Mutation Effects in Protein Kinases. Comput. Math. Methods Medicine 2014: 653487:1-653487:24 (2014) - [j10]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) - 2013
- [j9]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): 2962-2978 (2013) - 2012
- [j8]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): 2501-2515 (2012) - 2011
- [j7]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) - 2009
- [j6]Gennady Verkhivker:
Computational proteomics analysis of binding mechanisms and molecular signatures of the HIV-1 protease drugs. Artif. Intell. Medicine 45(2-3): 197-206 (2009) - [j5]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) - [j4]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) - 2007
- [j3]Gennady Verkhivker:
Exploring sequence-structure relationships in the tyrosine kinome space: functional classification of the binding specificity mechanisms for cancer therapeutics. Bioinform. 23(15): 1919-1926 (2007) - 2006
- [j2]Gennady Verkhivker:
Imprint of evolutionary conservation and protein structure variation on the binding function of protein tyrosine kinases. Bioinform. 22(15): 1846-1854 (2006) - 2000
- [j1]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): 731-751 (2000)
Conference and Workshop Papers
- 2016
- [c6]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: 45-56 - 2008
- [c5]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: 1-12 - [c4]Gennady Verkhivker:
Coarse-Grained Modeling of the HIV-1 Protease Binding Mechanisms: II. Folding Inhibition. CIBB 2008: 13-24 - 2007
- [c3]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: 604-611 - 1999
- [c2]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: 426-437 - 1995
- [c1]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: 615-627
Editorship
- 2009
- [e1]Francesco Masulli, Roberto Tagliaferri, Gennady Verkhivker:
Computational Intelligence Methods for Bioinformatics and Biostatistics, 5th International Meeting, CIBB 2008, Vietri sul Mare, Italy, October 3-4, 2008, Revised Selected Papers. Lecture Notes in Computer Science 5488, Springer 2009, ISBN 978-3-642-02503-7 [contents]
Coauthor Index
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last updated on 2024-10-07 22:18 CEST by the dblp team
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