BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

213 related articles for article (PubMed ID: 30069648)

  • 1. Generating conformational transition paths with low potential-energy barriers for proteins.
    Nguyen MK; Jaillet L; Redon S
    J Comput Aided Mol Des; 2018 Aug; 32(8):853-867. PubMed ID: 30069648
    [TBL] [Abstract][Full Text] [Related]  

  • 2. As-Rigid-As-Possible molecular interpolation paths.
    Nguyen MK; Jaillet L; Redon S
    J Comput Aided Mol Des; 2017 Apr; 31(4):403-417. PubMed ID: 28321532
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.
    Seyler SL; Kumar A; Thorpe MF; Beckstein O
    PLoS Comput Biol; 2015 Oct; 11(10):e1004568. PubMed ID: 26488417
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Direct determination of reaction paths and stationary points on potential of mean force surfaces.
    Li G; Cui Q
    J Mol Graph Model; 2005 Oct; 24(2):82-93. PubMed ID: 16005650
    [TBL] [Abstract][Full Text] [Related]  

  • 5. ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths.
    Nguyen MK; Jaillet L; Redon S
    J Comput Aided Mol Des; 2019 Aug; 33(8):705-727. PubMed ID: 31435895
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Using robotics to fold proteins and dock ligands.
    Brutlag D; Apaydin S; Guestrin C; Hsu D; Varma C; Singh A; Latombe JC
    Bioinformatics; 2002; 18 Suppl 2():S74. PubMed ID: 12385986
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.
    Molloy K; Shehu A
    BMC Struct Biol; 2013; 13 Suppl 1(Suppl 1):S8. PubMed ID: 24565158
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Accurate free energy calculation along optimized paths.
    Chen C; Xiao Y
    J Comput Chem; 2010 May; 31(7):1368-75. PubMed ID: 19859916
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin.
    Ovchinnikov V; Karplus M
    J Phys Chem B; 2012 Jul; 116(29):8584-603. PubMed ID: 22409258
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes.
    Xie L; Liu H; Yang W
    J Chem Phys; 2004 May; 120(17):8039-52. PubMed ID: 15267723
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Nudged-elastic band used to find reaction coordinates based on the free energy.
    Bohner MU; Zeman J; Smiatek J; Arnold A; Kästner J
    J Chem Phys; 2014 Feb; 140(7):074109. PubMed ID: 24559340
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Improved initial guess for minimum energy path calculations.
    Smidstrup S; Pedersen A; Stokbro K; Jónsson H
    J Chem Phys; 2014 Jun; 140(21):214106. PubMed ID: 24907989
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Protein Conformational Transitions from All-Atom Adaptively Biased Path Optimization.
    Wu H; Post CB
    J Chem Theory Comput; 2018 Oct; 14(10):5372-5382. PubMed ID: 30222340
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair.
    Mathews DH; Case DA
    J Mol Biol; 2006 Apr; 357(5):1683-93. PubMed ID: 16487974
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Coarse-grained free energy functions for studying protein conformational changes: a double-well network model.
    Chu JW; Voth GA
    Biophys J; 2007 Dec; 93(11):3860-71. PubMed ID: 17704151
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Minimum action transition paths connecting minima on an energy surface.
    Koehl P
    J Chem Phys; 2016 Nov; 145(18):184111. PubMed ID: 27846680
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Fast exploration of an optimal path on the multidimensional free energy surface.
    Chen C
    PLoS One; 2017; 12(5):e0177740. PubMed ID: 28542475
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Free-end adaptive nudged elastic band method for locating transition states in minimum energy path calculation.
    Zhang J; Zhang H; Ye H; Zheng Y
    J Chem Phys; 2016 Sep; 145(9):094104. PubMed ID: 27608986
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Smooth Rotation Enhanced As-Rigid-As-Possible Mesh Animation.
    Levi Z; Gotsman C
    IEEE Trans Vis Comput Graph; 2015 Feb; 21(2):264-77. PubMed ID: 26357035
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Path optimization by a variational reaction coordinate method. II. Improved computational efficiency through internal coordinates and surface interpolation.
    Birkholz AB; Schlegel HB
    J Chem Phys; 2016 May; 144(18):184101. PubMed ID: 27179465
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 11.