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140 related items for PubMed ID: 37352129

  • 1. Comparing the influence of explicit and implicit solvation models on site-specific thermodynamic stability of proteins.
    Cho MK, Chong SH, Ham S, Shin S.
    J Comput Chem; 2023 Sep 30; 44(25):1976-1985. PubMed ID: 37352129
    [Abstract] [Full Text] [Related]

  • 2. Free energy landscape of protein folding in water: explicit vs. implicit solvent.
    Zhou R.
    Proteins; 2003 Nov 01; 53(2):148-61. PubMed ID: 14517967
    [Abstract] [Full Text] [Related]

  • 3. Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation.
    Roe DR, Okur A, Wickstrom L, Hornak V, Simmerling C.
    J Phys Chem B; 2007 Feb 22; 111(7):1846-57. PubMed ID: 17256983
    [Abstract] [Full Text] [Related]

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  • 5. Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.
    Deng N, Zhang BW, Levy RM.
    J Chem Theory Comput; 2015 Jun 09; 11(6):2868-78. PubMed ID: 26236174
    [Abstract] [Full Text] [Related]

  • 6. Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.
    Katkova EV, Onufriev AV, Aguilar B, Sulimov VB.
    J Mol Graph Model; 2017 Mar 09; 72():70-80. PubMed ID: 28064081
    [Abstract] [Full Text] [Related]

  • 7. Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models.
    Cumberworth A, Bui JM, Gsponer J.
    J Comput Chem; 2016 Mar 15; 37(7):629-40. PubMed ID: 26558440
    [Abstract] [Full Text] [Related]

  • 8. Why Computed Protein Folding Landscapes Are Sensitive to the Water Model.
    Anandakrishnan R, Izadi S, Onufriev AV.
    J Chem Theory Comput; 2019 Jan 08; 15(1):625-636. PubMed ID: 30514080
    [Abstract] [Full Text] [Related]

  • 9. Generalized Born Implicit Solvent Models for Biomolecules.
    Onufriev AV, Case DA.
    Annu Rev Biophys; 2019 May 06; 48():275-296. PubMed ID: 30857399
    [Abstract] [Full Text] [Related]

  • 10. Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions.
    Chen J, Brooks CL.
    Phys Chem Chem Phys; 2008 Jan 28; 10(4):471-81. PubMed ID: 18183310
    [Abstract] [Full Text] [Related]

  • 11. Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.
    Izadi S, Aguilar B, Onufriev AV.
    J Chem Theory Comput; 2015 Sep 08; 11(9):4450-9. PubMed ID: 26575935
    [Abstract] [Full Text] [Related]

  • 12. Force field influences in beta-hairpin folding simulations.
    Lwin TZ, Luo R.
    Protein Sci; 2006 Nov 08; 15(11):2642-55. PubMed ID: 17075138
    [Abstract] [Full Text] [Related]

  • 13. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model.
    Vorobjev YN, Almagro JC, Hermans J.
    Proteins; 1998 Sep 01; 32(4):399-413. PubMed ID: 9726412
    [Abstract] [Full Text] [Related]

  • 14. Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?
    Zhou R, Berne BJ.
    Proc Natl Acad Sci U S A; 2002 Oct 01; 99(20):12777-82. PubMed ID: 12242327
    [Abstract] [Full Text] [Related]

  • 15. Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment.
    Kent A, Jha AK, Fitzgerald JE, Freed KF.
    J Phys Chem B; 2008 May 15; 112(19):6175-86. PubMed ID: 18348560
    [Abstract] [Full Text] [Related]

  • 16. Computational protein design is a challenge for implicit solvation models.
    Jaramillo A, Wodak SJ.
    Biophys J; 2005 Jan 15; 88(1):156-71. PubMed ID: 15377512
    [Abstract] [Full Text] [Related]

  • 17. Anti-cooperativity and cooperativity in hydrophobic interactions: Three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins.
    Shimizu S, Chan HS.
    Proteins; 2002 Jul 01; 48(1):15-30. PubMed ID: 12012334
    [Abstract] [Full Text] [Related]

  • 18. Evaluating the dynamics and electrostatic interactions of folded proteins in implicit solvents.
    Hua DP, Huang H, Roy A, Post CB.
    Protein Sci; 2016 Jan 01; 25(1):204-18. PubMed ID: 26189497
    [Abstract] [Full Text] [Related]

  • 19. Comparison of volume and surface area nonpolar solvation free energy terms for implicit solvent simulations.
    Lee MS, Olson MA.
    J Chem Phys; 2013 Jul 28; 139(4):044119. PubMed ID: 23901972
    [Abstract] [Full Text] [Related]

  • 20. Solvation Thermodynamics of Solutes in Water and Ionic Liquids Using the Multiscale Solvation-Layer Interface Condition Continuum Model.
    Rahimi AM, Jamali S, Bardhan JP, Lustig SR.
    J Chem Theory Comput; 2022 Sep 13; 18(9):5539-5558. PubMed ID: 36001344
    [Abstract] [Full Text] [Related]

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