Verkhivker G - Search Results

1

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.

Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. Xiao S, et al. Among authors: verkhivker g. J Chem Inf Model. 2023 Aug 28;63(16):5272-5296. doi: 10.1021/acs.jcim.3c00778. Epub 2023 Aug 7. J Chem Inf Model. 2023. PMID: 37549201 Free PMC article.

2

Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions.

Verkhivker GM, Rejto PA, Bouzida D, Arthurs S, Colson AB, Freer ST, Gehlhaar DK, Larson V, Luty BA, Marrone T, Rose PW. Verkhivker GM, et al. J Mol Recognit. 1999 Nov-Dec;12(6):371-89. doi: 10.1002/(SICI)1099-1352(199911/12)12:6<371::AID-JMR479>3.0.CO;2-O. J Mol Recognit. 1999. PMID: 10611647 Review.

3

Cancer driver mutations in protein kinase genes.

Torkamani A, Verkhivker G, Schork NJ. Torkamani A, et al. Among authors: verkhivker g. Cancer Lett. 2009 Aug 28;281(2):117-27. doi: 10.1016/j.canlet.2008.11.008. Epub 2008 Dec 10. Cancer Lett. 2009. PMID: 19081671 Free PMC article. Review.

4

Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.

Rejto PA, Verkhivker GM. Rejto PA, et al. Among authors: verkhivker gm. Proc Natl Acad Sci U S A. 1996 Aug 20;93(17):8945-50. doi: 10.1073/pnas.93.17.8945. Proc Natl Acad Sci U S A. 1996. PMID: 8799133 Free PMC article.

5

Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer.

Morra G, Verkhivker G, Colombo G. Morra G, et al. Among authors: verkhivker g. PLoS Comput Biol. 2009 Mar;5(3):e1000323. doi: 10.1371/journal.pcbi.1000323. Epub 2009 Mar 20. PLoS Comput Biol. 2009. PMID: 19300478 Free PMC article.

6

Understanding ligand-based modulation of the Hsp90 molecular chaperone dynamics at atomic resolution.

Colombo G, Morra G, Meli M, Verkhivker G. Colombo G, et al. Among authors: verkhivker g. Proc Natl Acad Sci U S A. 2008 Jun 10;105(23):7976-81. doi: 10.1073/pnas.0802879105. Epub 2008 May 29. Proc Natl Acad Sci U S A. 2008. PMID: 18511558 Free PMC article.

7

Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective.

Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Freer ST, Rose PW. Verkhivker GM, et al. Curr Opin Struct Biol. 2002 Apr;12(2):197-203. doi: 10.1016/s0959-440x(02)00310-x. Curr Opin Struct Biol. 2002. PMID: 11959497 Review.

8

Empirical free energy calculations of human immunodeficiency virus type 1 protease crystallographic complexes. II. Knowledge-based ligand-protein interaction potentials applied to thermodynamic analysis of hydrophobic mutations.

Verkhivker GM. Verkhivker GM. Pac Symp Biocomput. 1996:638-52. Pac Symp Biocomput. 1996. PMID: 9390264 Free article.

9

A systematic protocol for the characterization of Hsp90 modulators.

Matts RL, Brandt GE, Lu Y, Dixit A, Mollapour M, Wang S, Donnelly AC, Neckers L, Verkhivker G, Blagg BS. Matts RL, et al. Among authors: verkhivker g. Bioorg Med Chem. 2011 Jan 1;19(1):684-92. doi: 10.1016/j.bmc.2010.10.029. Epub 2010 Oct 19. Bioorg Med Chem. 2011. PMID: 21129982 Free PMC article.

10

Hierarchy of simulation models in predicting structure and energetics of the Src SH2 domain binding to tyrosyl phosphopeptides.

Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Schaffer L, Arthurs S, Colson AB, Freer ST, Larson V, Luty BA, Marrone T, Rose PW. Verkhivker GM, et al. J Med Chem. 2002 Jan 3;45(1):72-89. doi: 10.1021/jm0101141. J Med Chem. 2002. PMID: 11754580

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