Who We Are
The challenge of understanding biological systems at the molecular and systems level as well as the integration of computational and experimental approaches for bridging basic and clinical cancer research is what motivates our vibrant research group. Our scientific interests and research efforts are in the areas of Computational Cancer Biology and Pharmacogenetics, Computational Genomics and Pharmacology, Translational Bioinformatics and Computational Medicine with the focus on the development and integration of computational and experimental approaches for (a) system-based analysis of evolutionary, genetic, molecular and clinical signatures associated with human disease; (b) modeling of complex phenotypes and prediction of cancer biomarkers; (c) design and discovery of targeted and personalized cancer therapeutics and development of expert systems for personalized medicine; (d) integration of computational biology and translational informaticswith chemical biology and chemical genomics in translational cancer research; (e) enabling information-driven biomedical research on the “bench to bedside” path.
Molecular Recognition and Energy Landcapes
- Dixit, A, G. Verkhivker. The energy landscape analysis of cancer mutations in protein kinases.PLoS One. 2011;6(10):e26071. Epub 2011 Oct 6 [pdf]
Protein Kinases: Sturcture, Dynamics and Drug Design
- Dixit A, Verkhivker GM. 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):e1000487, 2009.[pdf]
- A. Dixit, , G. Verkhivker. 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. Epub 2011 Oct 6.[pdf]
Hsp90 Molecular Chaperone: Structure, Dynamics and Drug Design
Morra G, Verkhivker G, Colombo G. Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer.. PLoS Comput. Biol.5(3):e1000323, 2009. [pdf]
- G. Morra, M. A. C. Neves, C. J. Plescia, S. Tsustsumi, L. Neckers, G.M. Verkhivker, D. C. Altieri, G. Colombo. 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.[pdf]
- R. L. Matts, A. Dixit, L.B. Peterson, L. Sun, S. Voruganti, . Kalyanaraman, S. D. Hartson, G. M. Verkhivker, B. S. J. Blagg. Elucidation and assessment of the Hsp90 C-terminal inhibitor binding site. ACS Chem Biol. 2011 Aug 19;6(8):800-7. Epub 2011 May 17.[pdf]
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. PMID: 23977182.
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. PMID: 24466147.