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.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

145 related articles for article (PubMed ID: 28837923)

  • 1. Structural transition of solvated H-Ras/GTP revealed by molecular dynamics simulation and local network entropy.
    Matsunaga S; Hano Y; Saito Y; Fujimoto KJ; Kumasaka T; Matsumoto S; Kataoka T; Shima F; Tanaka S
    J Mol Graph Model; 2017 Oct; 77():51-63. PubMed ID: 28837923
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Hybrid QM/MM vs Pure MM Molecular Dynamics for Evaluating Water Distribution within p21
    Tichauer RH; Favre G; Cabantous S; Brut M
    J Phys Chem B; 2019 May; 123(18):3935-3944. PubMed ID: 30991803
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Calculation of pathways for the conformational transition between the GTP- and GDP-bound states of the Ha-ras-p21 protein: calculations with explicit solvent simulations and comparison with calculations in vacuum.
    Diaz JF; Wroblowski B; Schlitter J; Engelborghs Y
    Proteins; 1997 Jul; 28(3):434-51. PubMed ID: 9223188
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Probing the wild-type HRas activation mechanism using steered molecular dynamics, understanding the energy barrier and role of water in the activation.
    Sharma N; Sonavane U; Joshi R
    Eur Biophys J; 2014 Mar; 43(2-3):81-95. PubMed ID: 24442446
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Critical roles of interactions among switch I-preceding residues and between switch II and its neighboring alpha-helix in conformational dynamics of the GTP-bound Ras family small GTPases.
    Matsumoto K; Shima F; Muraoka S; Araki M; Hu L; Ijiri Y; Hirai R; Liao J; Yoshioka T; Kumasaka T; Yamamoto M; Tamura A; Kataoka T
    J Biol Chem; 2011 Apr; 286(17):15403-12. PubMed ID: 21388959
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations.
    Grigorenko BL; Nemukhin AV; Shadrina MS; Topol IA; Burt SK
    Proteins; 2007 Feb; 66(2):456-66. PubMed ID: 17094109
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Structural insight into the rearrangement of the switch I region in GTP-bound G12A K-Ras.
    Xu S; Long BN; Boris GH; Chen A; Ni S; Kennedy MA
    Acta Crystallogr D Struct Biol; 2017 Dec; 73(Pt 12):970-984. PubMed ID: 29199977
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Conformational and Dynamical Effects of Tyr32 Phosphorylation in K-Ras: Molecular Dynamics Simulation and Markov State Models Analysis.
    Khaled M; Gorfe A; Sayyed-Ahmad A
    J Phys Chem B; 2019 Sep; 123(36):7667-7675. PubMed ID: 31419909
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Oncogenic G12D mutation alters local conformations and dynamics of K-Ras.
    Vatansever S; Erman B; Gümüş ZH
    Sci Rep; 2019 Aug; 9(1):11730. PubMed ID: 31409810
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Distinct dynamics and interaction patterns in H- and K-Ras oncogenic P-loop mutants.
    Sayyed-Ahmad A; Prakash P; Gorfe AA
    Proteins; 2017 Sep; 85(9):1618-1632. PubMed ID: 28498561
    [TBL] [Abstract][Full Text] [Related]  

  • 11. QM/MM modeling the Ras-GAP catalyzed hydrolysis of guanosine triphosphate.
    Grigorenko BL; Nemukhin AV; Topol IA; Cachau RE; Burt SK
    Proteins; 2005 Aug; 60(3):495-503. PubMed ID: 15906320
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Hydrogen Bonding and Related Properties in Liquid Water: A Car-Parrinello Molecular Dynamics Simulation Study.
    Guardia E; Skarmoutsos I; Masia M
    J Phys Chem B; 2015 Jul; 119(29):8926-38. PubMed ID: 25313871
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Unveiling conformational dynamics changes of H-Ras induced by mutations based on accelerated molecular dynamics.
    Chen J; Wang W; Pang L; Zhu W
    Phys Chem Chem Phys; 2020 Sep; 22(37):21238-21250. PubMed ID: 32930679
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Configurational Disorder of Water Hydrogen-Bond Network at the Protein Dynamical Transition.
    Rahaman O; Kalimeri M; Katava M; Paciaroni A; Sterpone F
    J Phys Chem B; 2017 Jul; 121(28):6792-6798. PubMed ID: 28635287
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Role of the switch II region in the conformational transition of activation of Ha-ras-p21.
    Díaz JF; Escalona MM; Kuppens S; Engelborghs Y
    Protein Sci; 2000 Feb; 9(2):361-8. PubMed ID: 10716188
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Crystal structures of the state 1 conformations of the GTP-bound H-Ras protein and its oncogenic G12V and Q61L mutants.
    Muraoka S; Shima F; Araki M; Inoue T; Yoshimoto A; Ijiri Y; Seki N; Tamura A; Kumasaka T; Yamamoto M; Kataoka T
    FEBS Lett; 2012 Jun; 586(12):1715-8. PubMed ID: 22584058
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach.
    Gohlke H; Kuhn LA; Case DA
    Proteins; 2004 Aug; 56(2):322-37. PubMed ID: 15211515
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Structural dynamics of supercooled water from quasielastic neutron scattering and molecular simulations.
    Qvist J; Schober H; Halle B
    J Chem Phys; 2011 Apr; 134(14):144508. PubMed ID: 21495765
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins.
    Harada R; Shigeta Y
    J Comput Chem; 2017 Dec; 38(31):2671-2674. PubMed ID: 28861895
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Parallel Cascade Selection Molecular Dynamics (PaCS-MD) to generate conformational transition pathway.
    Harada R; Kitao A
    J Chem Phys; 2013 Jul; 139(3):035103. PubMed ID: 23883057
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.