219 related articles for article (PubMed ID: 35839100)
1. 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
Phys Chem Chem Phys; 2022 Jul; 24(29):17723-17743. PubMed ID: 35839100
[TBL] [Abstract][Full Text] [Related]
2. Conformational Flexibility and Local Frustration in the Functional States of the SARS-CoV-2 Spike B.1.1.7 and B.1.351 Variants: Mutation-Induced Allosteric Modulation Mechanism of Functional Dynamics and Protein Stability.
Verkhivker G
Int J Mol Sci; 2022 Jan; 23(3):. PubMed ID: 35163572
[TBL] [Abstract][Full Text] [Related]
3. Dynamic Network Modeling of Allosteric Interactions and Communication Pathways in the SARS-CoV-2 Spike Trimer Mutants: Differential Modulation of Conformational Landscapes and Signal Transmission via Cascades of Regulatory Switches.
Verkhivker GM; Di Paola L
J Phys Chem B; 2021 Jan; 125(3):850-873. PubMed ID: 33448856
[TBL] [Abstract][Full Text] [Related]
4. Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers: Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants.
Verkhivker G; Alshahrani M; Gupta G
Int J Mol Sci; 2023 Apr; 24(7):. PubMed ID: 37047615
[TBL] [Abstract][Full Text] [Related]
5. Comparative Analysis of Conformational Dynamics and Systematic Characterization of Cryptic Pockets in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 Spike Complexes with the ACE2 Host Receptor: Confluence of Binding and Structural Plasticity in Mediating Networks of Conserved Allosteric Sites.
Alshahrani M; Gupta G; Xiao S; Tao P; Verkhivker G
Viruses; 2023 Oct; 15(10):. PubMed ID: 37896850
[TBL] [Abstract][Full Text] [Related]
6. Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant.
Verkhivker G
Int J Mol Sci; 2022 Feb; 23(4):. PubMed ID: 35216287
[TBL] [Abstract][Full Text] [Related]
7. Exploring Conformational Landscapes and Cryptic Binding Pockets in Distinct Functional States of the SARS-CoV-2 Omicron BA.1 and BA.2 Trimers: Mutation-Induced Modulation of Protein Dynamics and Network-Guided Prediction of Variant-Specific Allosteric Binding Sites.
Verkhivker G; Alshahrani M; Gupta G
Viruses; 2023 Sep; 15(10):. PubMed ID: 37896786
[TBL] [Abstract][Full Text] [Related]
8. 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
Biomolecules; 2022 Jul; 12(7):. PubMed ID: 35883520
[TBL] [Abstract][Full Text] [Related]
9. Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes.
Verkhivker G; Alshahrani M; Gupta G
Viruses; 2023 May; 15(5):. PubMed ID: 37243229
[TBL] [Abstract][Full Text] [Related]
10. 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
J Biomol Struct Dyn; 2022; 40(20):9724-9741. PubMed ID: 34060425
[TBL] [Abstract][Full Text] [Related]
11. 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
J Chem Inf Model; 2022 Apr; 62(8):1956-1978. PubMed ID: 35377633
[TBL] [Abstract][Full Text] [Related]
12. Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike Proteins.
Verkhivker GM
J Proteome Res; 2020 Nov; 19(11):4587-4608. PubMed ID: 33006900
[TBL] [Abstract][Full Text] [Related]
13. Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms.
Xiao S; Alshahrani M; Gupta G; Tao P; Verkhivker G
J Chem Inf Model; 2023 Aug; 63(16):5272-5296. PubMed ID: 37549201
[TBL] [Abstract][Full Text] [Related]
14. 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
bioRxiv; 2023 Sep; ():. PubMed ID: 37745525
[TBL] [Abstract][Full Text] [Related]
15. 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
Int J Mol Sci; 2022 Sep; 23(19):. PubMed ID: 36232845
[TBL] [Abstract][Full Text] [Related]
16. Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships.
Verkhivker G; Alshahrani M; Gupta G; Xiao S; Tao P
Phys Chem Chem Phys; 2023 Aug; 25(32):21245-21266. PubMed ID: 37548589
[TBL] [Abstract][Full Text] [Related]
17. Exploring Binding Pockets in the Conformational States of the SARS-CoV-2 Spike Trimers for the Screening of Allosteric Inhibitors Using Molecular Simulations and Ensemble-Based Ligand Docking.
Gupta G; Verkhivker G
Int J Mol Sci; 2024 May; 25(9):. PubMed ID: 38732174
[TBL] [Abstract][Full Text] [Related]
18. AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape.
Raisinghani N; Alshahrani M; Gupta G; Xiao S; Tao P; Verkhivker G
J Chem Inf Model; 2024 Mar; 64(5):1657-1681. PubMed ID: 38373700
[TBL] [Abstract][Full Text] [Related]
19. 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
J Chem Inf Model; 2021 Oct; 61(10):5172-5191. PubMed ID: 34551245
[TBL] [Abstract][Full Text] [Related]
20. Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations.
Verkhivker G; Agajanian S; Kassab R; Krishnan K
Int J Mol Sci; 2022 Apr; 23(8):. PubMed ID: 35457196
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
