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235 related items for PubMed ID: 15481091

  • 1. Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method.
    Prabhu NV, Zhu P, Sharp KA.
    J Comput Chem; 2004 Dec; 25(16):2049-64. PubMed ID: 15481091
    [Abstract] [Full Text] [Related]

  • 2. Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules.
    Prabhu NV, Panda M, Yang Q, Sharp KA.
    J Comput Chem; 2008 May; 29(7):1113-30. PubMed ID: 18074338
    [Abstract] [Full Text] [Related]

  • 3. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.
    Hassan SA, Mehler EL, Zhang D, Weinstein H.
    Proteins; 2003 Apr 01; 51(1):109-25. PubMed ID: 12596268
    [Abstract] [Full Text] [Related]

  • 4. 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]

  • 5. How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis.
    Tan C, Yang L, Luo R.
    J Phys Chem B; 2006 Sep 21; 110(37):18680-7. PubMed ID: 16970499
    [Abstract] [Full Text] [Related]

  • 6. An efficient mean solvation force model for use in molecular dynamics simulations of proteins in aqueous solution.
    Fraternali F, Van Gunsteren WF.
    J Mol Biol; 1996 Mar 15; 256(5):939-48. PubMed ID: 8601844
    [Abstract] [Full Text] [Related]

  • 7. Quantitative analysis of Poisson-Boltzmann implicit solvent in molecular dynamics.
    Wang J, Tan C, Chanco E, Luo R.
    Phys Chem Chem Phys; 2010 Feb 07; 12(5):1194-202. PubMed ID: 20094685
    [Abstract] [Full Text] [Related]

  • 8. Protein molecular dynamics with electrostatic force entirely determined by a single Poisson-Boltzmann calculation.
    Lu BZ, Chen WZ, Wang CX, Xu XJ.
    Proteins; 2002 Aug 15; 48(3):497-504. PubMed ID: 12112674
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  • 12. FACTS: Fast analytical continuum treatment of solvation.
    Haberthür U, Caflisch A.
    J Comput Chem; 2008 Apr 15; 29(5):701-15. PubMed ID: 17918282
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  • 14. An evaluation of implicit and explicit solvent model systems for the molecular dynamics simulation of bacteriophage T4 lysozyme.
    Arnold GE, Ornstein RL.
    Proteins; 1994 Jan 15; 18(1):19-33. PubMed ID: 8146120
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  • 15. A semi-implicit solvent model for the simulation of peptides and proteins.
    Basdevant N, Borgis D, Ha-Duong T.
    J Comput Chem; 2004 Jun 15; 25(8):1015-29. PubMed ID: 15067677
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  • 16. Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations.
    Guvench O, Brooks CL.
    J Comput Chem; 2004 Jun 15; 25(8):1005-14. PubMed ID: 15067676
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  • 17. An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design.
    Vizcarra CL, Zhang N, Marshall SA, Wingreen NS, Zeng C, Mayo SL.
    J Comput Chem; 2008 May 15; 29(7):1153-62. PubMed ID: 18074340
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  • 18. All-atom fast protein folding simulations: the villin headpiece.
    Shen MY, Freed KF.
    Proteins; 2002 Dec 01; 49(4):439-45. PubMed ID: 12402354
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