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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. Among authors: agajanian s. Int J Mol Sci. 2022 Sep 29;23(19):11542. doi: 10.3390/ijms231911542. Int J Mol Sci. 2022. PMID: 36232845 Free PMC article.
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: agajanian s. 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.
Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies: Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations.
Verkhivker GM, Agajanian S, Oztas DY, Gupta G. Verkhivker GM, et al. Among authors: agajanian s. Biochemistry. 2021 May 18;60(19):1459-1484. doi: 10.1021/acs.biochem.1c00139. Epub 2021 Apr 26. Biochemistry. 2021. PMID: 33900725
Dynamic Profiling of Binding and Allosteric Propensities of the SARS-CoV-2 Spike Protein with Different Classes of Antibodies: Mutational and Perturbation-Based Scanning Reveals the Allosteric Duality of Functionally Adaptable Hotspots.
Verkhivker G, Agajanian S, Oztas D, Gupta G. Verkhivker G, et al. Among authors: agajanian s. J Chem Theory Comput. 2021 Jul 13;17(7):4578-4598. doi: 10.1021/acs.jctc.1c00372. Epub 2021 Jun 17. J Chem Theory Comput. 2021. PMID: 34138559
Allosteric Control of Structural Mimicry and Mutational Escape in the SARS-CoV-2 Spike Protein Complexes with the ACE2 Decoys and Miniprotein Inhibitors: A Network-Based Approach for Mutational Profiling of Binding and Signaling.
Verkhivker GM, Agajanian S, Oztas DY, Gupta G. Verkhivker GM, et al. Among authors: agajanian s. J Chem Inf Model. 2021 Oct 25;61(10):5172-5191. doi: 10.1021/acs.jcim.1c00766. Epub 2021 Sep 22. J Chem Inf Model. 2021. PMID: 34551245
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. Among authors: agajanian s. 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
Frustration-driven allosteric regulation and signal transmission in the SARS-CoV-2 spike omicron trimer structures: a crosstalk of the omicron mutation sites allosterically regulates tradeoffs of protein stability and conformational adaptability.
Verkhivker GM, Agajanian S, Kassab R, Krishnan K. Verkhivker GM, et al. Among authors: agajanian s. Phys Chem Chem Phys. 2022 Jul 27;24(29):17723-17743. doi: 10.1039/d2cp01893d. Phys Chem Chem Phys. 2022. PMID: 35839100
Integrating Conformational Dynamics and Perturbation-Based Network Modeling for Mutational Profiling of Binding and Allostery in the SARS-CoV-2 Spike Variant Complexes with Antibodies: Balancing Local and Global Determinants of Mutational Escape Mechanisms.
Verkhivker G, Agajanian S, Kassab R, Krishnan K. Verkhivker G, et al. Among authors: agajanian s. Biomolecules. 2022 Jul 10;12(7):964. doi: 10.3390/biom12070964. Biomolecules. 2022. PMID: 35883520 Free PMC article.
17 results