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Journal Abstract Search

742 related items for PubMed ID: 17119645

  • 21. Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: application to the TCR-p-MHC complex.
    Zoete V, Michielin O.
    Proteins; 2007 Jun 01; 67(4):1026-47. PubMed ID: 17377991
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  • 22. Solvation theory to provide a molecular interpretation of the hydrophobic entropy loss of noble-gas hydration.
    Irudayam SJ, Henchman RH.
    J Phys Condens Matter; 2010 Jul 21; 22(28):284108. PubMed ID: 21399280
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  • 23. Coupling nonpolar and polar solvation free energies in implicit solvent models.
    Dzubiella J, Swanson JM, McCammon JA.
    J Chem Phys; 2006 Feb 28; 124(8):084905. PubMed ID: 16512740
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  • 24. pH dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: application to 2'GMP/3'GMP binding to ribonuclease T1 and implications for catalysis.
    MacKerell AD, Sommer MS, Karplus M.
    J Mol Biol; 1995 Apr 07; 247(4):774-807. PubMed ID: 7723031
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  • 25. AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.
    Gallicchio E, Levy RM.
    J Comput Chem; 2004 Mar 07; 25(4):479-99. PubMed ID: 14735568
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  • 26. Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA.
    Baginski M, Fogolari F, Briggs JM.
    J Mol Biol; 1997 Nov 28; 274(2):253-67. PubMed ID: 9398531
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  • 27. Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters.
    Geerke DP, van Gunsteren WF.
    J Phys Chem B; 2007 Jun 14; 111(23):6425-36. PubMed ID: 17508737
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  • 28. Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes.
    Wan S, Stote RH, Karplus M.
    J Chem Phys; 2004 Nov 15; 121(19):9539-48. PubMed ID: 15538876
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  • 29. The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.
    Gallicchio E, Zhang LY, Levy RM.
    J Comput Chem; 2002 Apr 15; 23(5):517-29. PubMed ID: 11948578
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  • 30. Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy.
    Guvench O, Weiser J, Shenkin P, Kolossváry I, Still WC.
    J Comput Chem; 2002 Jan 30; 23(2):214-21. PubMed ID: 11924735
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  • 31. Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides.
    Pitera JW, Kollman PA.
    Proteins; 2000 Nov 15; 41(3):385-97. PubMed ID: 11025549
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  • 32. Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration.
    Genheden S, Mikulskis P, Hu L, Kongsted J, Söderhjelm P, Ryde U.
    J Am Chem Soc; 2011 Aug 24; 133(33):13081-92. PubMed ID: 21728337
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  • 33. Calculation of the hydration free energy difference between pyridine and its methyl-substituted derivatives by computer simulation methods.
    Partay L, Jedlovszky P, Jancsó G.
    J Phys Chem B; 2005 Apr 28; 109(16):8097-102. PubMed ID: 16851946
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  • 34. Evaluation of configurational entropy methods from peptide folding-unfolding simulation.
    Li DW, Khanlarzadeh M, Wang J, Huo S, Brüschweiler R.
    J Phys Chem B; 2007 Dec 13; 111(49):13807-13. PubMed ID: 18020439
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  • 35. Redox entropy of plastocyanin: developing a microscopic view of mesoscopic polar solvation.
    LeBard DN, Matyushov DV.
    J Chem Phys; 2008 Apr 21; 128(15):155106. PubMed ID: 18433287
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  • 36. Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials.
    Ge X, Roux B.
    J Mol Recognit; 2010 Apr 21; 23(2):128-41. PubMed ID: 20151411
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  • 37. Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions.
    Rosta E, Klähn M, Warshel A.
    J Phys Chem B; 2006 Feb 16; 110(6):2934-41. PubMed ID: 16471904
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  • 38. Configurational entropy and cooperativity between ligand binding and dimerization in glycopeptide antibiotics.
    Jusuf S, Loll PJ, Axelsen PH.
    J Am Chem Soc; 2003 Apr 02; 125(13):3988-94. PubMed ID: 12656635
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  • 39. The effect of water displacement on binding thermodynamics: concanavalin A.
    Li Z, Lazaridis T.
    J Phys Chem B; 2005 Jan 13; 109(1):662-70. PubMed ID: 16851059
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  • 40. Hydration in discrete water. A mean field, cellular automata based approach to calculating hydration free energies.
    Setny P, Zacharias M.
    J Phys Chem B; 2010 Jul 08; 114(26):8667-75. PubMed ID: 20552986
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