BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

309 related articles for article (PubMed ID: 18849406)

  • 1. Flexible fitting of high-resolution x-ray structures into cryoelectron microscopy maps using biased molecular dynamics simulations.
    Orzechowski M; Tama F
    Biophys J; 2008 Dec; 95(12):5692-705. PubMed ID: 18849406
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM.
    Tama F; Miyashita O; Brooks CL
    J Struct Biol; 2004 Sep; 147(3):315-26. PubMed ID: 15450300
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Biased coarse-grained molecular dynamics simulation approach for flexible fitting of X-ray structure into cryo electron microscopy maps.
    Grubisic I; Shokhirev MN; Orzechowski M; Miyashita O; Tama F
    J Struct Biol; 2010 Jan; 169(1):95-105. PubMed ID: 19800974
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Consensus among multiple approaches as a reliability measure for flexible fitting into cryo-EM data.
    Ahmed A; Tama F
    J Struct Biol; 2013 May; 182(2):67-77. PubMed ID: 23416197
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Accurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization.
    Zheng W
    Biophys J; 2011 Jan; 100(2):478-88. PubMed ID: 21244844
    [TBL] [Abstract][Full Text] [Related]  

  • 6. High-resolution modeling of protein structures based on flexible fitting of low-resolution structural data.
    Zheng W; Tekpinar M
    Adv Protein Chem Struct Biol; 2014; 96():267-84. PubMed ID: 25443961
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Refinement of Atomic Structures Against cryo-EM Maps.
    Murshudov GN
    Methods Enzymol; 2016; 579():277-305. PubMed ID: 27572731
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Consensus among flexible fitting approaches improves the interpretation of cryo-EM data.
    Ahmed A; Whitford PC; Sanbonmatsu KY; Tama F
    J Struct Biol; 2012 Feb; 177(2):561-70. PubMed ID: 22019767
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography.
    Trabuco LG; Villa E; Schreiner E; Harrison CB; Schulten K
    Methods; 2009 Oct; 49(2):174-80. PubMed ID: 19398010
    [TBL] [Abstract][Full Text] [Related]  

  • 10. NMMD: Efficient Cryo-EM Flexible Fitting Based on Simultaneous Normal Mode and Molecular Dynamics atomic displacements.
    Vuillemot R; Miyashita O; Tama F; Rouiller I; Jonic S
    J Mol Biol; 2022 Apr; 434(7):167483. PubMed ID: 35150654
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
    Trabuco LG; Villa E; Mitra K; Frank J; Schulten K
    Structure; 2008 May; 16(5):673-83. PubMed ID: 18462672
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Applications of the molecular dynamics flexible fitting method.
    Trabuco LG; Schreiner E; Gumbart J; Hsin J; Villa E; Schulten K
    J Struct Biol; 2011 Mar; 173(3):420-7. PubMed ID: 20932910
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences.
    Dou H; Burrows DW; Baker ML; Ju T
    Biophys J; 2017 Jun; 112(12):2479-2493. PubMed ID: 28636906
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Use of evolutionary information in the fitting of atomic level protein models in low resolution cryo-EM map of a protein assembly improves the accuracy of the fitting.
    Joseph AP; Swapna LS; Rakesh R; Srinivasan N
    J Struct Biol; 2016 Sep; 195(3):294-305. PubMed ID: 27444391
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions.
    Kirmizialtin S; Loerke J; Behrmann E; Spahn CMT; Sanbonmatsu KY
    Methods Enzymol; 2015; 558():497-514. PubMed ID: 26068751
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Acceleration of cryo-EM Flexible Fitting for Large Biomolecular Systems by Efficient Space Partitioning.
    Mori T; Kulik M; Miyashita O; Jung J; Tama F; Sugita Y
    Structure; 2019 Jan; 27(1):161-174.e3. PubMed ID: 30344106
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Domain motions of EF-G bound to the 70S ribosome: insights from a hand-shaking between multi-resolution structures.
    Wriggers W; Agrawal RK; Drew DL; McCammon A; Frank J
    Biophys J; 2000 Sep; 79(3):1670-8. PubMed ID: 10969026
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities.
    Leelananda SP; Lindert S
    J Chem Theory Comput; 2017 Oct; 13(10):5131-5145. PubMed ID: 28949136
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Accurate flexible refinement of atomic models against medium-resolution cryo-EM maps using damped dynamics.
    Kovacs JA; Galkin VE; Wriggers W
    BMC Struct Biol; 2018 Sep; 18(1):12. PubMed ID: 30219048
    [TBL] [Abstract][Full Text] [Related]  

  • 20. High-Resolution Cryo-EM Maps and Models: A Crystallographer's Perspective.
    Wlodawer A; Li M; Dauter Z
    Structure; 2017 Oct; 25(10):1589-1597.e1. PubMed ID: 28867613
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 16.