419 related articles for article (PubMed ID: 30339916)
1. Biophysical simulations and structure-based modeling of residue interaction networks in the tumor suppressor proteins reveal functional role of cancer mutation hotspots in molecular communication.
Verkhivker GM
Biochim Biophys Acta Gen Subj; 2019 Jan; 1863(1):210-225. PubMed ID: 30339916
[TBL] [Abstract][Full Text] [Related]
2. Conformational Dynamics and Allosteric Regulation Landscapes of Germline PTEN Mutations Associated with Autism Compared to Those Associated with Cancer.
Smith IN; Thacker S; Seyfi M; Cheng F; Eng C
Am J Hum Genet; 2019 May; 104(5):861-878. PubMed ID: 31006514
[TBL] [Abstract][Full Text] [Related]
3. Computational modeling of allosteric regulation in the hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric communications.
Blacklock K; Verkhivker GM
PLoS Comput Biol; 2014 Jun; 10(6):e1003679. PubMed ID: 24922508
[TBL] [Abstract][Full Text] [Related]
4. Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins.
Stetz G; Verkhivker GM
PLoS One; 2015; 10(11):e0143752. PubMed ID: 26619280
[TBL] [Abstract][Full Text] [Related]
5. 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
J Chem Inf Model; 2018 Oct; 58(10):2131-2150. PubMed ID: 30253099
[TBL] [Abstract][Full Text] [Related]
6. 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
J Chem Inf Model; 2013 Nov; 53(11):2962-78. PubMed ID: 24191708
[TBL] [Abstract][Full Text] [Related]
7. 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
J Chem Inf Model; 2015 Aug; 55(8):1645-62. PubMed ID: 26236953
[TBL] [Abstract][Full Text] [Related]
8. Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions.
James KA; Verkhivker GM
PLoS One; 2014; 9(11):e113488. PubMed ID: 25427151
[TBL] [Abstract][Full Text] [Related]
9. 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]
10. Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.
Stetz G; Verkhivker GM
PLoS Comput Biol; 2017 Jan; 13(1):e1005299. PubMed ID: 28095400
[TBL] [Abstract][Full Text] [Related]
11. Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways.
Tse A; Verkhivker GM
PLoS One; 2016; 11(11):e0166583. PubMed ID: 27861609
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone.
Stetz G; Tse A; Verkhivker GM
PLoS One; 2017; 12(11):e0186089. PubMed ID: 29095844
[TBL] [Abstract][Full Text] [Related]
14. Probing Allosteric Inhibition Mechanisms of the Hsp70 Chaperone Proteins Using Molecular Dynamics Simulations and Analysis of the Residue Interaction Networks.
Stetz G; Verkhivker GM
J Chem Inf Model; 2016 Aug; 56(8):1490-517. PubMed ID: 27447295
[TBL] [Abstract][Full Text] [Related]
15. Atomistic Modeling of the ABL Kinase Regulation by Allosteric Modulators Using Structural Perturbation Analysis and Community-Based Network Reconstruction of Allosteric Communications.
Astl L; Verkhivker GM
J Chem Theory Comput; 2019 May; 15(5):3362-3380. PubMed ID: 31017783
[TBL] [Abstract][Full Text] [Related]
16. 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]
17. 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]
18. 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]
19. Probing conformational landscapes and mechanisms of allosteric communication in the functional states of the ABL kinase domain using multiscale simulations and network-based mutational profiling of allosteric residue potentials.
Krishnan K; Tian H; Tao P; Verkhivker GM
J Chem Phys; 2022 Dec; 157(24):245101. PubMed ID: 36586979
[TBL] [Abstract][Full Text] [Related]
20. Deep mutational scanning and machine learning reveal structural and molecular rules governing allosteric hotspots in homologous proteins.
Leander M; Liu Z; Cui Q; Raman S
Elife; 2022 Oct; 11():. PubMed ID: 36226916
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
