Publications

2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2010 – 2011Before 2010

2018

 

S. Agajanian, O. Odeyemi, A. Sonnenschein, GM. Verkhivker. Machine Learning Algorithms for Prediction and Analysis of Cancer Driver Genes and Mutations. FRONTIERS IN MOLECULAR BIOSCIENCES Section “Biological Modeling and Simulation”. Special Issue “Machine Learning in Biomolecular Simulations”, 2018. Invited Contributed Article, submitted

G. Hu, Z. Liang, GM. Verkhivker. Integration of Protein Structure Network Approaches and Evolutionary Analysis into High-throughput Modeling of Protein Dynamics and Allosteric Regulations: theory, tools and applications. Briefings in Bioinformatics, 2018, submitted

Astl, L, Verkhivker GM. Data-Driven Computational Modeling of Allosteric Proteins by Exploring Dynamics, Co-evolution, and Residue Interaction Networks. J. Mol. Biol. 2018, submitted

Stetz G, Tse A, Bouz J, Agajanian S., Oluyemi O., Verkhivker GM. Allosteric Mechanisms of Protein Kinase Regulation and Drug Resistance: A Synergistic Perspective from Computational Systems Biology and Biophysical Studies. In Advances in Experimental Medicine and Biology Series, Protein Allostery in Drug Discovery, Springer-Nature, Eds. Jian Zhang and Ruth Nussinov, 2018, Invited Book Chapter, In press

Verkhivker GM. Biophysical Simulations and Structure-Based Modeling of Residue Interaction Networks in the Tumor Suppressor Proteins Reveal Functional Role of Cancer Mutation Hotspots in Molecular Communication. Biochimica et Biophysica Acta (BBA) – General Subjects. 2018, In press

H. Zhou, Z. Dong, GM. Verkhivker, BD. Zoltowski, P. Tao. Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis. Plos Comput. Biol. 2018, In press

Stetz G, Tse A, Bouz J, Verkhivker GM. Allosteric Mechanisms of BRAF Kinases Regulation and Combating Drug Resistance of Kinase Inhibitors: A Synergistic Perspective from Computational Systems Biology and Biophysical Studies. J. Mol. Biol. 2018, in press.

S. Agajanian, O. Odeyemi, N. Bischoff, S. Ratra, GM. 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. 2018, in press

Stetz G, Tse A, Verkhivker GM.Dissecting Structure-Encoded Determinants of Allosteric Cross-Talk between Post-Translational Modification Sites in the Hsp90 Chaperones.   Sci. Rep. 2018,  8 (1), 6899.

Verkhivker GM. Dynamics-based community analysis and perturbation response scanning of allosteric interaction networks in the TRAP1 chaperone structures dissect molecular linkage between conformational asymmetry and sequential ATP hydrolysis. Biochim Biophys Acta. 2018 Apr 20. pii: S1570-9639(18)30049-9. doi: 10.1016/j.bbapap.2018.04.008.

Stetz G, Verkhivker GM. 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. 2018 Feb 26;58(2):405-421. doi: 10.1021/acs.jcim.7b00638. Epub 2018 Feb 15.

Verkhivker GM.Computational Modeling of the Hsp90 Interactions with Cochaperones and Small-Molecule Inhibitors. Methods Mol Biol. 2018;1709:253-273. doi: 10.1007/978-1-4939-7477-1_19.

2017

Czemeres J, Buse K, Verkhivker GM. Atomistic simulations and network-based modeling of the Hsp90-Cdc37 chaperone binding with Cdk4 client protein: A mechanism of chaperoning kinase clients by exploiting weak spots of intrinsically dynamic kinase domains. PLoS One. 2017 Dec 21;12(12):e0190267. doi: 10.1371/journal.pone.0190267. eCollection 2017.

Stetz G, Tse A, Verkhivker GM.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. PLoS One. 2017 Nov 2;12(11):e0186089. doi: 10.1371/journal.pone.0186089. eCollection 2017.

GM Verkhivker.  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. Mol Biosyst. 2017 Oct 24;13(11):2235-2253. doi: 10.1039/c7mb00355b.

GM Verkhivker, K. Blacklock, G. Stetz. Computational Modeling of the Hsp90 Interactions with Cochaperones and Small Molecule Inhibitors, Methods in Molecular Biology,Chaperones : Methods and Protocols. Editors: Calderwood, Stuart K., Prince, Thomas L. (Eds.)

Stetz G, Verkhivker GM.  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. 2017 Jan 17;13(1):e1005299. doi: 10.1371/journal.pcbi.1005299. eCollection 2017 Jan. PMID: 28095400

Tiwari RK, Brown A, Sadeghiani N, Shirazi AN, Bolton J, Tse A, Verkhivker G, Parang K, Sun G.Design, Synthesis, and Evaluation of Dasatinib-Amino Acid and Dasatinib-Fatty Acid Conjugates as Protein Tyrosine Kinase Inhibitors. ChemMedChem. 2017 Jan 5;12(1):86-99. doi: 10.1002/cmdc.201600387. Epub 2016 Dec 5.

 

2016

Tiwari RK, Brown A, Sadeghiani N, Shirazi AN, Bolton J, Tse A, Verkhivker GM, Parang K, Sun G. Design, Synthesis, and Evaluation of Dasatinib-Amino Acid and Dasatinib-Fatty Acid Conjugates as Protein Tyrosine Kinase Inhibitors. ChemMedChem , 2016 Nov 22. PUBMED.

Abstract

 

Verkhivker GM. Leveraging Structural Diversity and Allosteric Regulatory Mechanisms of Protein Kinases in the Discovery of Small Molecule Inhibitors. Curr Med Chem . 2016 Oct 6. [Epub ahead of print] PUBMED

Abstract

 

Tse A, Verkhivker GM. 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. Plos ONE , 2016, Nov 18;11(11):e0166583. PUBMED.

Abstract

 

Verkhivker GM. Molecular dynamics simulations and modelling of the residue interaction networks in the BRAF kinase complexes with small molecule inhibitors: probing the allosteric effects of ligand-induced kinase dimerization and paradoxical activation. Mol Biosyst . 2016 Oct 20;12(10):3146-65. PUBMED.

Abstract

 

Stetz G, Verkhivker GM. Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks. J Chem Inf Model. 2016 Aug 22;56(8):1490-517. PUBMED.

Abstract

 

Verkhivker GM.Integrating genetic and structural data on human protein kinome in network-based modeling of kinase sensitivities and resistance to targeted and personalized anticancer drugs. Pac Symp Biocomput. 2016; 21:45-56. PUBMED.

Abstract

 

2015

Stetz G, Verkhivker GM. Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins. PLoS One. 2015 Nov 30;10(11):e0143752. PUBMED.

Abstract

 

Tse A, Verkhivker GM. 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. 2015 Aug 24;55(8):1645-62. Epub 2015 Aug 12. PUBMED.

Abstract

 

Tse A, Verkhivker GM. Small-world networks of residue interactions in the Abl kinase complexes with cancer drugs: topology of allosteric communication pathways can determine drug resistance effects. Mol Biosyst. 2015 Jul;11(7):2082-95. PUBMED.

Abstract

 

Tse A, Verkhivker GM. 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. PLoS One. 2015 Jun 15;10(6):e0130203. eCollection 2015. PUBMED.

Abstract

 

2014

James KA, Verkhivker GM. 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. PLoS One. 2014 Nov26;9(11):3113488. doi:10.1371/journal.pone.0113488. eCollection 2014. PUBMED.

Abstract

 

Verkhivker GM. 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. Israel Journal of Chemistry. Special Issue: Computational Molecular Biophysics Volume 54, Issue 8-9, pages 1052–1064, August 2014.

Abstract

 

Blacklock K, Verkhivker GM. Computational modeling of allosteric regulation in the hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric communications. PLoS Comput Biol. 2014 Jun 12;10(6):e1003679. doi: 10.1371/journal.pcbi.1003679. eCollection 2014 Jun. PUBMED.

Abstract

 

Dixit A, Verkhivker GM. Structure-functional prediction and analysis of cancer mutation effects in protein kinases. Comput Math Methods Med. 2014;2014:653487. doi: 10.1155/2014/653487. Epub 2014 Apr 8. PUBMED.

Abstract

 

Blacklock K, Verkhivker GM. Allosteric regulation of the Hsp90 dynamics and stability by client recruiter cochaperones: protein structure network modeling. PLoS One. 2014 Jan 20;9(1):e86547. doi: 10.1371/journal.pone.0086547. eCollection 2014. PUBMED.

Abstract

 

2013

Lawless N, Blacklock K, Berrigan E, Verkhivker GM. 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. Pharmaceuticals (Basel). 2013 Nov 11;6(11):1407-28. doi: 10.3390/ph6111407. PUBMED.

Abstract

 

Blacklock K, Verkhivker GM. 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. 2013 Nov 25;53(11):2962-78. doi: 10.1021/ci400434g. Epub 2013 Nov 12. PUBMED.

Abstract

 

Blacklock K, Verkhivker GM. Differential modulation of functional dynamics and allosteric interactions in the Hsp90-cochaperone complexes with p23 and Aha1: a computational study. PLoS One. 2013 Aug 19;8(8):e71936. doi: 10.1371/journal.pone.0071936. eCollection 2013. PUBMED.

Abstract

 

2012

Dixit A, Verkhivker GM. Integrating ligand-based and protein-centric virtual screening of kinase inhibitors using ensembles of multiple protein kinase genes and conformations. J Chem Inf Model. 2012 Oct 22;52(10):2501-15. doi: 10.1021/ci3002638. Epub 2012 Oct 1. PUBMED.

Abstract

 

Verkhivker GM. Simulating Molecular Mechanisms of the MDM2-Mediated Regulatory Interactions: A Conformational Selection Model of the MDM2 Lid Dynamics. Plos One 2012;7(7):e40897. Epub 2012 Jul 16. PUBMED.

Abstract

 

Dixit A, Verkhivker GM. Probing molecular mechanisms of the hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics. PLoS One. 2012;7(5):e37605. Epub 2012 May 18. PUBMED.

Abstract

 

2010 – 2011

Dixit A, Verkhivker GM.The energy landscape analysis of cancer mutations in protein kinases. PLoS One. 2011;6(10):e26071. PUBMED.

Abstract

 

Dixit A, Verkhivker GM. Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases. PLoS Comput Biol. 2011 Oct;7(10):e1002179. PUBMED.

Abstract

 

Matts RL, Dixit A, Peterson LB, Sun L, Voruganti S, Kalyanaraman, Hartson SD, Verkhivker GM, Blagg BSJ. Elucidation and assessment of the Hsp90 C-terminal inhibitor binding site. ACS Chem Biol. 2011 Aug 19;6(8):800-807. PUBMED.

Abstract

 

Matts RL, Brandt GEL, Lu Y, Dixit A, Mollapour M, Wang S, Donnelly AC, Neckers L, Verkhivker GM, Blagg BSJ. A systematic protocol for the characterization of Hsp90 modulators. Bioorg Med Chem. 2011 19(1):684-92. PUBMED.

Abstract

 

Friedman A, Torkamani A, Verkhivker GM, Schork NJ. From coding variants to structure and function insights. In the book “Protein Structure” Ed.Lauren M. Haggerty Series: Protein Science and Engineering Nova Science Publishers, 2011.

Abstract

 

Morra G, Neves MAC, Plescia CJ, Tsustsumi C, Neckers L, Verkhivker GM, Altieri DC, Colombo G. Dynamics-Based Discovery of Allosteric Inhibitors: Selection of New Ligands for the C-terminal Domain of Hsp90. J. Chem. Theory Comput. , 6 : 2978–2989, 2010. PUBMED.

Abstract

 

Before 2010