Verkhivker G - Search Results

1

Integrated Computational Approaches and Tools forAllosteric Drug Discovery.

Sheik Amamuddy O, Veldman W, Manyumwa C, Khairallah A, Agajanian S, Oluyemi O, Verkhivker G, Tastan Bishop O. Sheik Amamuddy O, et al. Among authors: verkhivker g. Int J Mol Sci. 2020 Jan 28;21(3):847. doi: 10.3390/ijms21030847. Int J Mol Sci. 2020. PMID: 32013012 Free PMC article. Review.

2

Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes.

Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Alshahrani M, et al. Among authors: verkhivker g. bioRxiv [Preprint]. 2023 Sep 12:2023.09.11.557205. doi: 10.1101/2023.09.11.557205. bioRxiv. 2023. PMID: 37745525 Free PMC article. Preprint.

3

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. Tse A, et al. Among authors: verkhivker gm. Mol Biosyst. 2015 Jul;11(7):2082-95. doi: 10.1039/c5mb00246j. Mol Biosyst. 2015. PMID: 25996455

4

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.

Verkhivker GM. Verkhivker GM. Mol Biosyst. 2016 Oct 20;12(10):3146-65. doi: 10.1039/c6mb00298f. Epub 2016 Aug 2. Mol Biosyst. 2016. PMID: 27481329

5

Leveraging Structural Diversity and Allosteric Regulatory Mechanisms of Protein Kinases in the Discovery of Small Molecule Inhibitors.

Verkhivker GM. Verkhivker GM. Curr Med Chem. 2017;24(42):4838-4872. doi: 10.2174/0929867323666161006113418. Curr Med Chem. 2017. PMID: 27719654 Review.

6

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.

Verkhivker GM. Verkhivker GM. Mol Biosyst. 2017 Oct 24;13(11):2235-2253. doi: 10.1039/c7mb00355b. Mol Biosyst. 2017. PMID: 28926061

7

Computational Modeling of the Hsp90 Interactions with Cochaperones and Small-Molecule Inhibitors.

Verkhivker GM. Verkhivker GM. Methods Mol Biol. 2018;1709:253-273. doi: 10.1007/978-1-4939-7477-1_19. Methods Mol Biol. 2018. PMID: 29177665

8

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.

Agajanian S, Odeyemi O, Bischoff N, Ratra S, Verkhivker GM. Agajanian S, et al. J Chem Inf Model. 2018 Oct 22;58(10):2131-2150. doi: 10.1021/acs.jcim.8b00414. Epub 2018 Oct 3. J Chem Inf Model. 2018. PMID: 30253099

9

Integration of network models and evolutionary analysis into high-throughput modeling of protein dynamics and allosteric regulation: theory, tools and applications.

Liang Z, Verkhivker GM, Hu G. Liang Z, et al. Among authors: verkhivker gm. Brief Bioinform. 2020 May 21;21(3):815-835. doi: 10.1093/bib/bbz029. Brief Bioinform. 2020. PMID: 30911759 Review.

10

Integration of Random Forest Classifiers and Deep Convolutional Neural Networks for Classification and Biomolecular Modeling of Cancer Driver Mutations.

Agajanian S, Oluyemi O, Verkhivker GM. Agajanian S, et al. Front Mol Biosci. 2019 Jun 11;6:44. doi: 10.3389/fmolb.2019.00044. eCollection 2019. Front Mol Biosci. 2019. PMID: 31245384 Free PMC article.

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