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Journal Abstract Search

288 related items for PubMed ID: 21341292

  • 1. A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets.
    Mukherjee G, Patra N, Barua P, Jayaram B.
    J Comput Chem; 2011 Apr 15; 32(5):893-907. PubMed ID: 21341292
    [Abstract] [Full Text] [Related]

  • 2. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.
    Jakalian A, Jack DB, Bayly CI.
    J Comput Chem; 2002 Dec 15; 23(16):1623-41. PubMed ID: 12395429
    [Abstract] [Full Text] [Related]

  • 3. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.
    Mobley DL, Dumont E, Chodera JD, Dill KA.
    J Phys Chem B; 2007 Mar 08; 111(9):2242-54. PubMed ID: 17291029
    [Abstract] [Full Text] [Related]

  • 4. 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]

  • 5. Atoms-in-molecules study of the genetically encoded amino acids. III. Bond and atomic properties and their correlations with experiment including mutation-induced changes in protein stability and genetic coding.
    Matta CF, Bader RF.
    Proteins; 2003 Aug 15; 52(3):360-99. PubMed ID: 12866050
    [Abstract] [Full Text] [Related]

  • 6. Computational protocol for predicting the binding affinities of zinc containing metalloprotein-ligand complexes.
    Jain T, Jayaram B.
    Proteins; 2007 Jun 01; 67(4):1167-78. PubMed ID: 17380508
    [Abstract] [Full Text] [Related]

  • 7. 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]

  • 8. A new force field (ECEPP-05) for peptides, proteins, and organic molecules.
    Arnautova YA, Jagielska A, Scheraga HA.
    J Phys Chem B; 2006 Mar 16; 110(10):5025-44. PubMed ID: 16526746
    [Abstract] [Full Text] [Related]

  • 9. Development and testing of a general amber force field.
    Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA.
    J Comput Chem; 2004 Jul 15; 25(9):1157-74. PubMed ID: 15116359
    [Abstract] [Full Text] [Related]

  • 10. Communication: Quantum polarized fluctuating charge model: a practical method to include ligand polarizability in biomolecular simulations.
    Kimura SR, Rajamani R, Langley DR.
    J Chem Phys; 2011 Dec 21; 135(23):231101. PubMed ID: 22191857
    [Abstract] [Full Text] [Related]

  • 11. I-SOLV: a new surface-based empirical model for computing solvation free energies.
    Wang R, Lin F, Xu Y, Cheng T.
    J Mol Graph Model; 2007 Jul 21; 26(1):368-77. PubMed ID: 17317248
    [Abstract] [Full Text] [Related]

  • 12. Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations.
    Lin H, Truhlar DG.
    J Phys Chem A; 2005 May 05; 109(17):3991-4004. PubMed ID: 16833721
    [Abstract] [Full Text] [Related]

  • 13. Specific empirical free energy function for automated docking of carbohydrates to proteins.
    Laederach A, Reilly PJ.
    J Comput Chem; 2003 Nov 15; 24(14):1748-57. PubMed ID: 12964193
    [Abstract] [Full Text] [Related]

  • 14. Geometry optimization using tuned and balanced redistributed charge schemes for combined quantum mechanical and molecular mechanical calculations.
    Wang B, Truhlar DG.
    Phys Chem Chem Phys; 2011 Jun 14; 13(22):10556-64. PubMed ID: 21403957
    [Abstract] [Full Text] [Related]

  • 15. A general and fast scoring function for protein-ligand interactions: a simplified potential approach.
    Muegge I, Martin YC.
    J Med Chem; 1999 Mar 11; 42(5):791-804. PubMed ID: 10072678
    [Abstract] [Full Text] [Related]

  • 16. The treatment of solvation by a generalized Born model and a self-consistent charge-density functional theory-based tight-binding method.
    Xie L, Liu H.
    J Comput Chem; 2002 Nov 30; 23(15):1404-15. PubMed ID: 12370943
    [Abstract] [Full Text] [Related]

  • 17. Accuracy of free energies of hydration using CM1 and CM3 atomic charges.
    Udier-Blagović M, Morales De Tirado P, Pearlman SA, Jorgensen WL.
    J Comput Chem; 2004 Aug 30; 25(11):1322-32. PubMed ID: 15185325
    [Abstract] [Full Text] [Related]

  • 18. Hydrogen bonding of the nucleobase mimic 2-pyridone to fluorobenzenes: an ab initio investigation.
    Frey JA, Leist R, Leutwyler S.
    J Phys Chem A; 2006 Mar 30; 110(12):4188-95. PubMed ID: 16553369
    [Abstract] [Full Text] [Related]

  • 19. Ab initio quantum mechanical study of the binding energies of human estrogen receptor alpha with its ligands: an application of fragment molecular orbital method.
    Fukuzawa K, Kitaura K, Uebayasi M, Nakata K, Kaminuma T, Nakano T.
    J Comput Chem; 2005 Jan 15; 26(1):1-10. PubMed ID: 15521089
    [Abstract] [Full Text] [Related]

  • 20. Polarization charge densities provide a predictive quantification of hydrogen bond energies.
    Klamt A, Reinisch J, Eckert F, Hellweg A, Diedenhofen M.
    Phys Chem Chem Phys; 2012 Jan 14; 14(2):955-63. PubMed ID: 22120043
    [Abstract] [Full Text] [Related]

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