These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
283 related articles for article (PubMed ID: 34060425)
1. 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]
2. 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]
3. 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]
4. 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]
5. 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]
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. 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]
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. Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant. Verkhivker GM; Agajanian S; Oztas DY; Gupta G ACS Omega; 2021 Jun; 6(24):16216-16233. PubMed ID: 34179666 [TBL] [Abstract][Full Text] [Related]
10. 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 J Chem Theory Comput; 2021 Jul; 17(7):4578-4598. PubMed ID: 34138559 [TBL] [Abstract][Full Text] [Related]
11. 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 Biochemistry; 2021 May; 60(19):1459-1484. PubMed ID: 33900725 [TBL] [Abstract][Full Text] [Related]
12. 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]
13. 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]
14. 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]
15. 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]
17. Molecular characterization of interactions between the D614G variant of SARS-CoV-2 S-protein and neutralizing antibodies: A computational approach. Kwarteng A; Asiedu E; Sylverken AA; Larbi A; Sakyi SA; Asiedu SO Infect Genet Evol; 2021 Jul; 91():104815. PubMed ID: 33774178 [TBL] [Abstract][Full Text] [Related]
18. 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]
19. Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. Mahmoudi Gomari M; Rostami N; Omidi-Ardali H; Arab SS J Biomol Struct Dyn; 2022 Aug; 40(12):5634-5642. PubMed ID: 33475020 [TBL] [Abstract][Full Text] [Related]
20. AlphaFold2 Predictions of Conformational Ensembles and Atomistic Simulations of the SARS-CoV-2 Spike XBB Lineages Reveal Epistatic Couplings between Convergent Mutational Hotspots that Control ACE2 Affinity. Raisinghani N; Alshahrani M; Gupta G; Xiao S; Tao P; Verkhivker G J Phys Chem B; 2024 May; 128(19):4696-4715. PubMed ID: 38696745 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]