BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

185 related articles for article (PubMed ID: 26606367)

  • 1. Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides.
    Nerenberg PS; Head-Gordon T
    J Chem Theory Comput; 2011 Apr; 7(4):1220-30. PubMed ID: 26606367
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Conformational Preferences of an Intrinsically Disordered Protein Domain: A Case Study for Modern Force Fields.
    Gopal SM; Wingbermühle S; Schnatwinkel J; Juber S; Herrmann C; Schäfer LV
    J Phys Chem B; 2021 Jan; 125(1):24-35. PubMed ID: 33382616
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Comparison of hydration behavior and conformational preferences of the Trp-cage mini-protein in different rigid-body water models.
    Gupta M; Nayar D; Chakravarty C; Bandyopadhyay S
    Phys Chem Chem Phys; 2016 Dec; 18(48):32796-32813. PubMed ID: 27878168
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Optimizing solute-water van der Waals interactions to reproduce solvation free energies.
    Nerenberg PS; Jo B; So C; Tripathy A; Head-Gordon T
    J Phys Chem B; 2012 Apr; 116(15):4524-34. PubMed ID: 22443635
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Probing the functional conformations of an atypical proline-rich fusion peptide.
    Dutta N; Dutta Chowdhury S; Lahiri A
    Phys Chem Chem Phys; 2019 Sep; 21(37):20727-20742. PubMed ID: 31509121
    [TBL] [Abstract][Full Text] [Related]  

  • 6. 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]  

  • 7. Evaluating the performance of the ff99SB force field based on NMR scalar coupling data.
    Wickstrom L; Okur A; Simmerling C
    Biophys J; 2009 Aug; 97(3):853-6. PubMed ID: 19651043
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Influence of water-protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models.
    Paschek D; Day R; García AE
    Phys Chem Chem Phys; 2011 Nov; 13(44):19840-7. PubMed ID: 21845272
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Experimental verification of force fields for molecular dynamics simulations using Gly-Pro-Gly-Gly.
    Aliev AE; Courtier-Murias D
    J Phys Chem B; 2010 Sep; 114(38):12358-75. PubMed ID: 20825228
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Protein simulations with an optimized water model: cooperative helix formation and temperature-induced unfolded state collapse.
    Best RB; Mittal J
    J Phys Chem B; 2010 Nov; 114(46):14916-23. PubMed ID: 21038907
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models.
    Zhang H; Yin C; Jiang Y; van der Spoel D
    J Chem Inf Model; 2018 May; 58(5):1037-1052. PubMed ID: 29648448
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D.
    Grotz KK; Schwierz N
    J Chem Theory Comput; 2022 Jan; 18(1):526-537. PubMed ID: 34881568
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Systematic Differences between Current Molecular Dynamics Force Fields To Represent Local Properties of Intrinsically Disordered Proteins.
    Yu L; Li DW; Brüschweiler R
    J Phys Chem B; 2021 Jan; 125(3):798-804. PubMed ID: 33444020
    [TBL] [Abstract][Full Text] [Related]  

  • 14. The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development.
    Jiang F; Han W; Wu YD
    Phys Chem Chem Phys; 2013 Mar; 15(10):3413-28. PubMed ID: 23385383
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Sensitivity of local hydration behaviour and conformational preferences of peptides to choice of water model.
    Nayar D; Chakravarty C
    Phys Chem Chem Phys; 2014 Jun; 16(21):10199-213. PubMed ID: 24695799
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Balanced Solvent Model for Intrinsically Disordered and Ordered Proteins.
    Mu J; Pan Z; Chen HF
    J Chem Inf Model; 2021 Oct; 61(10):5141-5151. PubMed ID: 34546059
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact.
    Florová P; Sklenovský P; Banáš P; Otyepka M
    J Chem Theory Comput; 2010 Nov; 6(11):3569-79. PubMed ID: 26617103
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields.
    Mercadante D; Milles S; Fuertes G; Svergun DI; Lemke EA; Gräter F
    J Phys Chem B; 2015 Jun; 119(25):7975-84. PubMed ID: 26030189
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Well-Balanced Force Field
    Zhang Y; Liu H; Yang S; Luo R; Chen HF
    J Chem Theory Comput; 2019 Dec; 15(12):6769-6780. PubMed ID: 31657215
    [TBL] [Abstract][Full Text] [Related]  

  • 20. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.
    Maier JA; Martinez C; Kasavajhala K; Wickstrom L; Hauser KE; Simmerling C
    J Chem Theory Comput; 2015 Aug; 11(8):3696-713. PubMed ID: 26574453
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 10.