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 *

131 related articles for article (PubMed ID: 26580540)

  • 1. Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity.
    Paramo T; East A; Garzón D; Ulmschneider MB; Bond PJ
    J Chem Theory Comput; 2014 May; 10(5):2151-64. PubMed ID: 26580540
    [TBL] [Abstract][Full Text] [Related]  

  • 2. A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations.
    van Dijk M; Wassenaar TA; Bonvin AM
    J Chem Theory Comput; 2012 Oct; 8(10):3463-72. PubMed ID: 26592996
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Protein Fluctuations and Cavity Changes Relationship.
    Barletta GP; Fernandez-Alberti S
    J Chem Theory Comput; 2018 Feb; 14(2):998-1008. PubMed ID: 29262685
    [TBL] [Abstract][Full Text] [Related]  

  • 4. MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories.
    Schmidtke P; Bidon-Chanal A; Luque FJ; Barril X
    Bioinformatics; 2011 Dec; 27(23):3276-85. PubMed ID: 21967761
    [TBL] [Abstract][Full Text] [Related]  

  • 5. dxTuber: detecting protein cavities, tunnels and clefts based on protein and solvent dynamics.
    Raunest M; Kandt C
    J Mol Graph Model; 2011 Jun; 29(7):895-905. PubMed ID: 21420887
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Pocket-space maps to identify novel binding-site conformations in proteins.
    Craig IR; Pfleger C; Gohlke H; Essex JW; Spiegel K
    J Chem Inf Model; 2011 Oct; 51(10):2666-79. PubMed ID: 21910474
    [TBL] [Abstract][Full Text] [Related]  

  • 7. The importance of membrane defects-lessons from simulations.
    Bennett WF; Tieleman DP
    Acc Chem Res; 2014 Aug; 47(8):2244-51. PubMed ID: 24892900
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Structural characterization of the tunnels of Mycobacterium tuberculosis truncated hemoglobin N from molecular dynamics simulations.
    Daigle R; Guertin M; Lagüe P
    Proteins; 2009 May; 75(3):735-47. PubMed ID: 19003999
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Brownian dynamics simulations of the recognition of the scorpion toxin maurotoxin with the voltage-gated potassium ion channels.
    Fu W; Cui M; Briggs JM; Huang X; Xiong B; Zhang Y; Luo X; Shen J; Ji R; Jiang H; Chen K
    Biophys J; 2002 Nov; 83(5):2370-85. PubMed ID: 12414674
    [TBL] [Abstract][Full Text] [Related]  

  • 10. APL@Voro: a Voronoi-based membrane analysis tool for GROMACS trajectories.
    Lukat G; Krüger J; Sommer B
    J Chem Inf Model; 2013 Nov; 53(11):2908-25. PubMed ID: 24175728
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Quaternary-Linked Changes in Structure and Dynamics That Modulate O2 Migration within Hemoglobin's Gas Diffusion Tunnels.
    Shadrina MS; Peslherbe GH; English AM
    Biochemistry; 2015 Sep; 54(34):5268-78. PubMed ID: 26226318
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Volarea - a bioinformatics tool to calculate the surface area and the volume of molecular systems.
    Ribeiro JV; Tamames JA; Cerqueira NM; Fernandes PA; Ramos MJ
    Chem Biol Drug Des; 2013 Dec; 82(6):743-55. PubMed ID: 24164915
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Analysis of changes of cavity volumes in predefined directions of protein motions and cavity flexibility.
    Barletta GP; Barletta M; Saldaño TE; Fernandez-Alberti S
    J Comput Chem; 2022 Mar; 43(6):391-401. PubMed ID: 34962296
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Exploring cavity dynamics in biomolecular systems.
    Lindow N; Baum D; Bondar AN; Hege HC
    BMC Bioinformatics; 2013; 14 Suppl 19(Suppl 19):S5. PubMed ID: 24564434
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Molecular dynamics simulations of PNA-PNA and PNA-DNA duplexes by the use of new parameters implemented in the GROMACS package: a conformational and dynamics study.
    Autiero I; Saviano M; Langella E
    Phys Chem Chem Phys; 2014 Feb; 16(5):1868-74. PubMed ID: 24327011
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Enabling grand-canonical Monte Carlo: extending the flexibility of GROMACS through the GromPy python interface module.
    Pool R; Heringa J; Hoefling M; Schulz R; Smith JC; Feenstra KA
    J Comput Chem; 2012 May; 33(12):1207-14. PubMed ID: 22370965
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Dynamics, hydration, and motional averaging of a loop-gated artificial protein cavity: the W191G mutant of cytochrome c peroxidase in water as revealed by molecular dynamics simulations.
    Baron R; McCammon JA
    Biochemistry; 2007 Sep; 46(37):10629-42. PubMed ID: 17718514
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Omega currents in voltage-gated ion channels: what can we learn from uncovering the voltage-sensing mechanism using MD simulations?
    Tarek M; Delemotte L
    Acc Chem Res; 2013 Dec; 46(12):2755-62. PubMed ID: 23697886
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Molecular dynamics explorations of active site structure in designed and evolved enzymes.
    Osuna S; Jiménez-Osés G; Noey EL; Houk KN
    Acc Chem Res; 2015 Apr; 48(4):1080-9. PubMed ID: 25738880
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Structural models of the transmembrane region of voltage-gated and other K+ channels in open, closed, and inactivated conformations.
    Durell SR; Hao Y; Guy HR
    J Struct Biol; 1998; 121(2):263-84. PubMed ID: 9615442
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 7.