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 *

193 related articles for article (PubMed ID: 24620905)

  • 1. How accurately do current force fields predict experimental peptide conformations? An adiabatic free energy dynamics study.
    Tzanov AT; Cuendet MA; Tuckerman ME
    J Phys Chem B; 2014 Jun; 118(24):6539-52. PubMed ID: 24620905
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.
    Mackerell AD; Feig M; Brooks CL
    J Comput Chem; 2004 Aug; 25(11):1400-15. PubMed ID: 15185334
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Heating and flooding: a unified approach for rapid generation of free energy surfaces.
    Chen M; Cuendet MA; Tuckerman ME
    J Chem Phys; 2012 Jul; 137(2):024102. PubMed ID: 22803523
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Metadynamics as a tool for mapping the conformational and free-energy space of peptides--the alanine dipeptide case study.
    Vymetal J; Vondrásek J
    J Phys Chem B; 2010 Apr; 114(16):5632-42. PubMed ID: 20361773
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Helix-coil transition of alanine peptides in water: force field dependence on the folded and unfolded structures.
    Gnanakaran S; García AE
    Proteins; 2005 Jun; 59(4):773-82. PubMed ID: 15815975
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Conformational preferences of N-acetyl-L-leucine-N'-methylamide. Gas-phase and solution calculations on the model dipeptide.
    Masman MF; Lovas S; Murphy RF; Enriz RD; Rodríguez AM
    J Phys Chem A; 2007 Oct; 111(42):10682-91. PubMed ID: 17887655
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Efficient and direct generation of multidimensional free energy surfaces via adiabatic dynamics without coordinate transformations.
    Abrams JB; Tuckerman ME
    J Phys Chem B; 2008 Dec; 112(49):15742-57. PubMed ID: 19367870
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Assessment of the intrinsic conformational preferences of dipeptide amino acids in aqueous solution by combined umbrella sampling/MBAR statistics. A comparison with experimental results.
    Cruz VL; Ramos J; Martinez-Salazar J
    J Phys Chem B; 2012 Jan; 116(1):469-75. PubMed ID: 22136632
    [TBL] [Abstract][Full Text] [Related]  

  • 9. A comparative study of two different force fields on structural and thermodynamics character of H1 peptide via molecular dynamics simulations.
    Cao Z; Wang J
    J Biomol Struct Dyn; 2010 Apr; 27(5):651-61. PubMed ID: 20085382
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations.
    Ono S; Kuroda M; Higo J; Nakajima N; Nakamura H
    J Comput Chem; 2002 Mar; 23(4):470-6. PubMed ID: 11908083
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Reoptimization of the AMBER force field parameters for peptide bond (Omega) torsions using accelerated molecular dynamics.
    Doshi U; Hamelberg D
    J Phys Chem B; 2009 Dec; 113(52):16590-5. PubMed ID: 19938868
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.
    Peng X; Zhang Y; Chu H; Li G
    J Comput Chem; 2016 Mar; 37(6):614-22. PubMed ID: 26493154
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Reverse turns in blocked dipeptides are intrinsically unstable in water.
    Tobias DJ; Sneddon SF; Brooks CL
    J Mol Biol; 1990 Dec; 216(3):783-96. PubMed ID: 2258940
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Discrepancies between conformational distributions of a polyalanine peptide in solution obtained from molecular dynamics force fields and amide I' band profiles.
    Verbaro D; Ghosh I; Nau WM; Schweitzer-Stenner R
    J Phys Chem B; 2010 Dec; 114(51):17201-8. PubMed ID: 21138254
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables.
    Hashemian B; Millán D; Arroyo M
    J Chem Phys; 2013 Dec; 139(21):214101. PubMed ID: 24320358
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.
    Bonomi M; Barducci A; Parrinello M
    J Comput Chem; 2009 Aug; 30(11):1615-21. PubMed ID: 19421997
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution.
    Hu H; Elstner M; Hermans J
    Proteins; 2003 Feb; 50(3):451-63. PubMed ID: 12557187
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Mapping the backbone dihedral free-energy surfaces in small peptides in solution using adiabatic free-energy dynamics.
    Rosso L; Abrams JB; Tuckerman ME
    J Phys Chem B; 2005 Mar; 109(9):4162-7. PubMed ID: 16851477
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Helix formation in a pentapeptide: experiment and force-field dependent dynamics.
    Hegefeld WA; Chen SE; DeLeon KY; Kuczera K; Jas GS
    J Phys Chem A; 2010 Dec; 114(47):12391-402. PubMed ID: 21058639
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Effects of pH and temperature on the structural and thermodynamic character of alpha-syn12 peptide in aqueous solution.
    Cao Z; Liu L; Wang J
    J Biomol Struct Dyn; 2010 Dec; 28(3):343-53. PubMed ID: 20919750
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.