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366 related items for PubMed ID: 15382247

  • 1. Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?
    Morreale A, de la Cruz X, Meyer T, Gelpí JL, Luque FJ, Orozco M.
    Proteins; 2004 Nov 15; 57(3):458-67. PubMed ID: 15382247
    [Abstract] [Full Text] [Related]

  • 2. 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]

  • 3. FACTS: Fast analytical continuum treatment of solvation.
    Haberthür U, Caflisch A.
    J Comput Chem; 2008 Apr 15; 29(5):701-15. PubMed ID: 17918282
    [Abstract] [Full Text] [Related]

  • 4. Direct observation of salt effects on molecular interactions through explicit-solvent molecular dynamics simulations: differential effects on electrostatic and hydrophobic interactions and comparisons to Poisson-Boltzmann theory.
    Thomas AS, Elcock AH.
    J Am Chem Soc; 2006 Jun 21; 128(24):7796-806. PubMed ID: 16771493
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  • 5. 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]

  • 6. 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
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  • 7. Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.
    Simonson T, Carlsson J, Case DA.
    J Am Chem Soc; 2004 Apr 07; 126(13):4167-80. PubMed ID: 15053606
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  • 8. 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
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  • 9. Continuum solvation models in the linear interaction energy method.
    Carlsson J, Andér M, Nervall M, Aqvist J.
    J Phys Chem B; 2006 Jun 22; 110(24):12034-41. PubMed ID: 16800513
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  • 10. Incorporating receptor flexibility in the molecular design of protein interfaces.
    Li L, Liang S, Pilcher MM, Meroueh SO.
    Protein Eng Des Sel; 2009 Sep 22; 22(9):575-86. PubMed ID: 19643976
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  • 11. A semi-implicit solvent model for the simulation of peptides and proteins.
    Basdevant N, Borgis D, Ha-Duong T.
    J Comput Chem; 2004 Jun 22; 25(8):1015-29. PubMed ID: 15067677
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  • 12. Theory and applications of the generalized Born solvation model in macromolecular simulations.
    Tsui V, Case DA.
    Biopolymers; 2004 Jun 22; 56(4):275-91. PubMed ID: 11754341
    [Abstract] [Full Text] [Related]

  • 13. Partition of protein solvation into group contributions from molecular dynamics simulations.
    Morreale A, de la Cruz X, Meyer T, Gelpí JL, Luque FJ, Orozco M.
    Proteins; 2005 Jan 01; 58(1):101-9. PubMed ID: 15517587
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  • 14. Nonuniform charge scaling (NUCS): a practical approximation of solvent electrostatic screening in proteins.
    Schwarzl SM, Huang D, Smith JC, Fischer S.
    J Comput Chem; 2005 Oct 01; 26(13):1359-71. PubMed ID: 16021598
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  • 15. Evaluation of Poisson solvation models using a hybrid explicit/implicit solvent method.
    Lee MS, Olson MA.
    J Phys Chem B; 2005 Mar 24; 109(11):5223-36. PubMed ID: 16863188
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  • 16. Prediction of the binding energy for small molecules, peptides and proteins.
    Schapira M, Totrov M, Abagyan R.
    J Mol Recognit; 1999 Mar 24; 12(3):177-90. PubMed ID: 10398408
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  • 17. A comparative theoretical study of dipeptide solvation in water.
    Hugosson HW, Laio A, Maurer P, Rothlisberger U.
    J Comput Chem; 2006 Apr 15; 27(5):672-84. PubMed ID: 16477697
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  • 18. Calculating solvation energies by means of a fluctuating charge model combined with continuum solvent model.
    Zhao DX, Yu L, Gong LD, Liu C, Yang ZZ.
    J Chem Phys; 2011 May 21; 134(19):194115. PubMed ID: 21599052
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  • 19. 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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  • 20. Calculation of solvation free energy from quantum mechanical charge density and continuum dielectric theory.
    Wang M, Wong CF.
    J Phys Chem A; 2006 Apr 13; 110(14):4873-9. PubMed ID: 16599457
    [Abstract] [Full Text] [Related]

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