» Dr. Gennady Verkhivker

Schmid College of Science and Technology; Physics, Computational Science and Engineering
School of Pharmacy
Dr. Gennady Verkhivker
Office Location:
Hashinger Science Center 118
Lomonosov Moscow State University, Bachelor of Science
Lomonosov Moscow State University, Master of Science
Dr. Verkhivker is currently a Professor of Computational Biology. He is also an Adjunct Professor of Pharmacology at the Department of Pharmacology, UC San Diego. His research activities are in the areas of computational cancer biology, translational bioinformatics, and computational pharmacology. He received his PhD in Physical Chemistry from Moscow University and completed a postdoctoral fellowship in computational biophysics from University of Illinois at Chicago. In 2000-2005, Dr. Verkhivker has held various research and management positions at Pfizer Global Research and Development, San Diego.  Since 2002, he has been Adjunct Professor of Pharmacology at the Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego. In 2006, he joined School of Pharmacy and Center for Bioinformatics, The University of Kansas as a Professor of Pharmaceutical Chemistry and Bioinformatics. Dr. Verkhivker returned to California in 2011 and joined Chapman University in August 2011 as a Full Professor of Computational Biology. Upon arrival to Chapman, Dr. Verkhivker has established a dynamic research group engaged in translational research that attracted a large cohort of undergraduate and graduate students.  He has been involved in various global University initiatives and collaborations. Dr. Verkhivker has served on a number of important committees including Search Committee for new Found Dean of BioPharmacy School. He is also chairing the Doctoral Steering Committee of the newly approved PhD Graduate Program in Computational Sciences.
Recent Creative, Scholarly Work and Publications
Computational Modeling of the Hsp90 Interactions with Cochaperones and Small Molecule Inhibitors GM Verkhivker K. Blacklock, G. Stetz, Methods in Molecular Biology,Chaperones : Methods and Protocols. Editors: Calderwood, Stuart K., Prince, Thomas L. (Eds.)
Network-based modelling and percolation analysis of conformational dynamics and activation in the CDK2 and CDK4 proteins: Dynamic and energetic polarization of the kinase lobes may determine divergence of the regulatory mechanisms. GM Verkhivker. Mol Biosyst. 2017, Accepted, In press
Multiscale Simulations and Network-Centric Modeling of the Hsp90-Cdc37 Chaperone Interactions with Protein Kinase Clients: Atomistic Reconstruction of Allosteric Regulatory Mechanisms and Client Recruitment by the Chaperone Machine Gabrielle Stetz, Amanda Tse, G M. Verkhivker Plos Computational Biology, Accepted, In press
Ensemble-Based Modeling and Rigidity Decomposition of Allosteric Interaction Networks and Communication Pathways in Cyclin-Dependent Kinases: Differentiating Kinase Clients of the Hsp90-Cdc37 Chaperone. Gabrielle Stetz, Amanda Tse, G M. Verkhivker Plos ONE, Accepted, In press
Design, Synthesis, and Evaluation of Dasatinib-Amino Acid and Dasatinib-Fatty Acid Conjugates as Protein Tyrosine Kinase Inhibitors. Tiwari RK, Brown A, Sadeghiani N, Shirazi AN, Bolton J, Tse A, Verkhivker G, Parang K, Sun G. ChemMedChem. 2017 Jan 5;12(1):86-99. doi: 10.1002/cmdc.201600387. Epub 2016 Dec 5. PMID: 27875633
Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication. Stetz G, Verkhivker GM. PLoS Comput Biol. 2017 Jan 17;13(1):e1005299. doi: 10.1371/journal.pcbi.1005299. eCollection 2017 Jan. PMID: 28095400
Leveraging Structural Diversity and Allosteric Regulatory Mechanisms of Protein Kinases in the Discovery of Small Molecule Inhibitors. GM Verkhivker, Curr Med Chem. 2016 Oct 6 PMID: 27719654
Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways. Tse A, Verkhivker GM. PLoS One. 2016 Nov 18;11(11):e0166583. doi: 10.1371/journal.pone.0166583. eCollection 2016. PMID: 27861609
Allosteric Mechanisms of BRAF Kinases Regulation and Combating Drug Resistance of Kinase Inhibitors: A Synergistic Perspective from Computational Systems Biology and Biophysical Studies. Stetz G, Tse A, Bouz J, Verkhivker G. J. Mol. Biol. 2016, revision submitted
Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks. Stetz G, Verkhivker GM. J Chem Inf Model. 2016 Aug 22;56(8):1490-517. doi: 10.1021/acs.jcim.5b00755.
Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution. Tse A, Verkhivker GM. PLoS One. 2015 Jun 15;10(6):e0130203. doi: 10.1371/journal.pone.0130203. eCollection 2015. PMID: 26075886
Small-world networks of residue interactions in the Abl kinase complexes with cancer drugs: topology of allosteric communication pathways can determine drug resistance effects. Tse A, Verkhivker GM. Mol Biosyst. 2015 Jul;11(7):2082-95. doi: 10.1039/c5mb00246j. PMID: 25996455
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. Tse A, Verkhivker GM. J Chem Inf Model. 2015 Aug 24;55(8):1645-62. doi: 10.1021/acs.jcim.5b00240. Epub 2015 Aug 12. PMID: 26236953
A.Tse, K. Blacklock, GM. Verkhivker. Capturing Differential Sensitivity of Protein Kinases to Drug Binding and Mutations via Modeling of the Residue Interaction Networks and Allosteric Communication Pathways. Plos Computational Biology, 2015 , revision submitted
Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins. Stetz G, Verkhivker GM. PLoS One. 2015 Nov 30;10(11):e0143752. doi: 10.1371/journal.pone.0143752. eCollection 2015. PMID: 26619280
Computational modeling of Hsp90 molecular chaperone structure, dynamics and function: a synergistic perspective from biophysical simulations and systems biology analysis. N. Lawless, E. Berrigan, K. Blacklock, G. Verkhivker.Molecular Systems Biology, revision submitted
Google's long-term plan for extending human life. Verkhivker G. United Kingdom Centre for Policy Studies CapX • Sep 4, 2015. CapX is a British online news website and aggregator founded by the Centre for Policy Studies that offers original content, and features opinion from a wide-range of thinkers on politics, economics, and business issues.
Allosteric regulation of the Hsp90 dynamics and stability by client recruiter cochaperones: protein structure network modeling. Blacklock K, Verkhivker GM. PLoS One. 2014 Jan 20;9(1):e86547. doi: 10.1371/journal.pone.0086547. eCollection 2014. PMID: 24466147
Structure-functional prediction and analysis of cancer mutation effects in protein kinases. Dixit A, Verkhivker GM. Comput Math Methods Med. 2014;2014:653487. doi: 10.1155/2014/653487. Epub 2014 Apr 8. PMID: 24817905
Computational modeling of allosteric regulation in the hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric communications. Blacklock K, Verkhivker GM. PLoS Comput Biol. 2014 Jun 12;10(6):e1003679. doi: 10.1371/journal.pcbi.1003679. eCollection 2014 Jun. PMID: 24922508
Structure-Based Network Analysis of Activation Mechanisms in the ErbB Family of Receptor Tyrosine Kinases: The Regulatory Spine Residues Are Global Mediators of Structural Stability and Allosteric Interactions. James, K., Verkhivker GM. PLoS One. 2014 Nov 26;9(11):e113488. doi: 10.1371/journal.pone.0113488. eCollection 2014. PMID: 25427151
Computational Studies of Allosteric Regulation in the Hsp90 Molecular Chaperone: From Functional Dynamics and Protein Structure Networks to Allosteric Communications and Targeted Anti-Cancer Modulators. G. Verkhivker Israel Journal of Chemistry, 2014,special volume on "Computational Chemistry of Biomolecules" published online: 19 FEB 2014, DOI: 10.1002/ijch.201300143.
Differential modulation of functional dynamics and allosteric interactions in the Hsp90-cochaperone complexes with p23 and Aha1: a computational study. Blacklock K, Verkhivker GM. PLoS One. 2013 Aug 19;8(8):e71936. doi: 10.1371/journal.pone.0071936. eCollection 2013.
Experimentally guided structural modeling and dynamics analysis of Hsp90-p53 interactions: allosteric regulation of the Hsp90 chaperone by a client protein. Blacklock K, Verkhivker GM. J Chem Inf Model. 2013 Nov 25;53(11):2962-78. doi: 10.1021/ci400434g. Epub 2013 Nov 12. PMID: 24191708
Structural bioinformatics and protein docking analysis of the molecular chaperone-kinase interactions: towards allosteric inhibition of protein kinases by targeting the hsp90-cdc37 chaperone machinery. Lawless N, Blacklock K, Berrigan E, Verkhivker G. Pharmaceuticals (Basel). 2013 Nov 11;6(11):1407-28. doi: 10.3390/ph6111407. PMID: 24287464