Verkhivker GM - Search Results

1

Landscape-Based Protein Stability Analysis and Network Modeling of Multiple Conformational States of the SARS-CoV-2 Spike D614G Mutant: Conformational Plasticity and Frustration-Induced Allostery as Energetic Drivers of Highly Transmissible Spike Variants.

Verkhivker GM, Agajanian S, Kassab R, Krishnan K. Verkhivker GM, et al. J Chem Inf Model. 2022 Apr 25;62(8):1956-1978. doi: 10.1021/acs.jcim.2c00124. Epub 2022 Apr 4. J Chem Inf Model. 2022. PMID: 35377633

2

Experimentally guided structural modeling and dynamics analysis of Hsp90-p53 interactions: allosteric regulation of the Hsp90 chaperone by a client protein.

Blacklock K, Verkhivker GM. Blacklock K, et al. Among authors: verkhivker gm. J Chem Inf Model. 2013 Nov 25;53(11):2962-78. doi: 10.1021/ci400434g. Epub 2013 Nov 12. J Chem Inf Model. 2013. PMID: 24191708

3

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.

Tse A, Verkhivker GM. Tse A, et al. Among authors: verkhivker gm. J Chem Inf Model. 2015 Aug 24;55(8):1645-62. doi: 10.1021/acs.jcim.5b00240. Epub 2015 Aug 12. J Chem Inf Model. 2015. PMID: 26236953

4

Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks.

Stetz G, Verkhivker GM. Stetz G, et al. Among authors: verkhivker gm. J Chem Inf Model. 2016 Aug 22;56(8):1490-517. doi: 10.1021/acs.jcim.5b00755. Epub 2016 Aug 1. J Chem Inf Model. 2016. PMID: 27447295

5

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.

Stetz G, Verkhivker GM. Stetz G, et al. Among authors: verkhivker gm. J Chem Inf Model. 2018 Feb 26;58(2):405-421. doi: 10.1021/acs.jcim.7b00638. Epub 2018 Feb 15. J Chem Inf Model. 2018. PMID: 29432007

6

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. Among authors: verkhivker gm. 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

7

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. Among authors: verkhivker gm. 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.

8

Dynamic View of Allosteric Regulation in the Hsp70 Chaperones by J-Domain Cochaperone and Post-Translational Modifications: Computational Analysis of Hsp70 Mechanisms by Exploring Conformational Landscapes and Residue Interaction Networks.

Astl L, Verkhivker GM. Astl L, et al. Among authors: verkhivker gm. J Chem Inf Model. 2020 Mar 23;60(3):1614-1631. doi: 10.1021/acs.jcim.9b01045. Epub 2020 Jan 21. J Chem Inf Model. 2020. PMID: 31935082

9

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. 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.

10

Allosteric Mechanism of the Hsp90 Chaperone Interactions with Cochaperones and Client Proteins by Modulating Communication Spines of Coupled Regulatory Switches: Integrative Atomistic Modeling of Hsp90 Signaling in Dynamic Interaction Networks.

Astl L, Stetz G, Verkhivker GM. Astl L, et al. Among authors: verkhivker gm. J Chem Inf Model. 2020 Jul 27;60(7):3616-3631. doi: 10.1021/acs.jcim.0c00380. Epub 2020 Jun 18. J Chem Inf Model. 2020. PMID: 32519853

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