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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.
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.
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
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
Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation.
Verkhivker GM, Agajanian S, Oztas D, Gupta G. Verkhivker GM, et al. Among authors: agajanian s. J Biomol Struct Dyn. 2022;40(20):9724-9741. doi: 10.1080/07391102.2021.1933594. Epub 2021 Jun 1. J Biomol Struct Dyn. 2022. PMID: 34060425
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
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