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 *

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.