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695 related items for PubMed ID: 17238257

  • 1. Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space.
    Naïm M, Bhat S, Rankin KN, Dennis S, Chowdhury SF, Siddiqi I, Drabik P, Sulea T, Bayly CI, Jakalian A, Purisima EO.
    J Chem Inf Model; 2007; 47(1):122-33. PubMed ID: 17238257
    [Abstract] [Full Text] [Related]

  • 2. Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 2. Benchmark in the CSAR-2010 scoring exercise.
    Sulea T, Cui Q, Purisima EO.
    J Chem Inf Model; 2011 Sep 26; 51(9):2066-81. PubMed ID: 21714553
    [Abstract] [Full Text] [Related]

  • 3. Estimating protein-ligand binding free energy: atomic solvation parameters for partition coefficient and solvation free energy calculation.
    Pei J, Wang Q, Zhou J, Lai L.
    Proteins; 2004 Dec 01; 57(4):651-64. PubMed ID: 15390269
    [Abstract] [Full Text] [Related]

  • 4. What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?
    Wang W, Wang J, Kollman PA.
    Proteins; 1999 Feb 15; 34(3):395-402. PubMed ID: 10024025
    [Abstract] [Full Text] [Related]

  • 5. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches.
    Miyamoto S, Kollman PA.
    Proteins; 1993 Jul 15; 16(3):226-45. PubMed ID: 8346190
    [Abstract] [Full Text] [Related]

  • 6. Prediction of ligand binding affinity and orientation of xenoestrogens to the estrogen receptor by molecular dynamics simulations and the linear interaction energy method.
    van Lipzig MM, ter Laak AM, Jongejan A, Vermeulen NP, Wamelink M, Geerke D, Meerman JH.
    J Med Chem; 2004 Feb 12; 47(4):1018-30. PubMed ID: 14761204
    [Abstract] [Full Text] [Related]

  • 7. Prediction of ligand-receptor binding thermodynamics by free energy force field three-dimensional quantitative structure-activity relationship analysis: applications to a set of glucose analogue inhibitors of glycogen phosphorylase.
    Venkatarangan P, Hopfinger AJ.
    J Med Chem; 1999 Jun 17; 42(12):2169-79. PubMed ID: 10377222
    [Abstract] [Full Text] [Related]

  • 8. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease.
    Sham YY, Chu ZT, Tao H, Warshel A.
    Proteins; 2000 Jun 01; 39(4):393-407. PubMed ID: 10813821
    [Abstract] [Full Text] [Related]

  • 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
    [Abstract] [Full Text] [Related]

  • 10. Linear interaction energy models for beta-secretase (BACE) inhibitors: Role of van der Waals, electrostatic, and continuum-solvation terms.
    Tounge BA, Rajamani R, Baxter EW, Reitz AB, Reynolds CH.
    J Mol Graph Model; 2006 May 22; 24(6):475-84. PubMed ID: 16293430
    [Abstract] [Full Text] [Related]

  • 11. 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
    [Abstract] [Full Text] [Related]

  • 12. An all atom energy based computational protocol for predicting binding affinities of protein-ligand complexes.
    Jain T, Jayaram B.
    FEBS Lett; 2005 Dec 05; 579(29):6659-66. PubMed ID: 16307743
    [Abstract] [Full Text] [Related]

  • 13. Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies.
    Genheden S, Ryde U.
    Proteins; 2012 May 05; 80(5):1326-42. PubMed ID: 22274991
    [Abstract] [Full Text] [Related]

  • 14. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions.
    Marenich AV, Cramer CJ, Truhlar DG.
    J Phys Chem B; 2009 May 07; 113(18):6378-96. PubMed ID: 19366259
    [Abstract] [Full Text] [Related]

  • 15. 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
    [Abstract] [Full Text] [Related]

  • 16. PEARLS: program for energetic analysis of receptor-ligand system.
    Han LY, Lin HH, Li ZR, Zheng CJ, Cao ZW, Xie B, Chen YZ.
    J Chem Inf Model; 2006 Jun 14; 46(1):445-50. PubMed ID: 16426079
    [Abstract] [Full Text] [Related]

  • 17. On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.
    Levy RM, Zhang LY, Gallicchio E, Felts AK.
    J Am Chem Soc; 2003 Aug 06; 125(31):9523-30. PubMed ID: 12889983
    [Abstract] [Full Text] [Related]

  • 18. The consequences of scoring docked ligand conformations using free energy correlations.
    Spyrakis F, Amadasi A, Fornabaio M, Abraham DJ, Mozzarelli A, Kellogg GE, Cozzini P.
    Eur J Med Chem; 2007 Jul 06; 42(7):921-33. PubMed ID: 17346861
    [Abstract] [Full Text] [Related]

  • 19. Aqueous solvation free energies of ions and ion-water clusters based on an accurate value for the absolute aqueous solvation free energy of the proton.
    Kelly CP, Cramer CJ, Truhlar DG.
    J Phys Chem B; 2006 Aug 17; 110(32):16066-81. PubMed ID: 16898764
    [Abstract] [Full Text] [Related]

  • 20. Assessing scoring functions for protein-ligand interactions.
    Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL.
    J Med Chem; 2004 Jun 03; 47(12):3032-47. PubMed ID: 15163185
    [Abstract] [Full Text] [Related]

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