Verkhivker G - Search Results

1

Probing Mechanisms of Binding and Allostery in the SARS-CoV-2 Spike Omicron Variant Complexes with the Host Receptor: Revealing Functional Roles of the Binding Hotspots in Mediating Epistatic Effects and Communication with Allosteric Pockets.

Verkhivker G, Agajanian S, Kassab R, Krishnan K. Verkhivker G, et al. Int J Mol Sci. 2022 Sep 29;23(19):11542. doi: 10.3390/ijms231911542. Int J Mol Sci. 2022. PMID: 36232845 Free PMC article.

2

Microsecond Molecular Dynamics Simulations and Markov State Models of Mutation-Induced Allosteric Mechanisms for the Light-Oxygen-Voltage 2 Protein : Revealing Structural Basis of Signal Transmission Induced by Photoactivation of the Light Protein State.

Xiao S, Ibrahim MT, Verkhivker GM, Zoltowski BD, Tao P. Xiao S, et al. Among authors: verkhivker gm. bioRxiv [Preprint]. 2023 Dec 23:2023.12.22.573121. doi: 10.1101/2023.12.22.573121. bioRxiv. 2023. PMID: 38187662 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

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

6

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.

7

Establishing Computational Approaches Towards Identifying Malarial Allosteric Modulators: A Case Study of Plasmodium falciparum Hsp70s.

Amusengeri A, Astl L, Lobb K, Verkhivker GM, Tastan Bishop Ö. Amusengeri A, et al. Int J Mol Sci. 2019 Nov 8;20(22):5574. doi: 10.3390/ijms20225574. Int J Mol Sci. 2019. PMID: 31717270 Free PMC article.

8

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.

9

Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning.

Verkhivker GM, Agajanian S, Hu G, Tao P. Verkhivker GM, et al. Front Mol Biosci. 2020 Jul 9;7:136. doi: 10.3389/fmolb.2020.00136. eCollection 2020. Front Mol Biosci. 2020. PMID: 32733918 Free PMC article. Review.

10

Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M^pro.

Sheik Amamuddy O, Verkhivker GM, Tastan Bishop Ö. Sheik Amamuddy O, et al. J Chem Inf Model. 2020 Oct 26;60(10):5080-5102. doi: 10.1021/acs.jcim.0c00634. Epub 2020 Sep 16. J Chem Inf Model. 2020. PMID: 32853525 Free PMC article.

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