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585 related items for PubMed ID: 16805629

  • 1. New-generation amber united-atom force field.
    Yang L, Tan CH, Hsieh MJ, Wang J, Duan Y, Cieplak P, Caldwell J, Kollman PA, Luo R.
    J Phys Chem B; 2006 Jul 06; 110(26):13166-76. PubMed ID: 16805629
    [Abstract] [Full Text] [Related]

  • 2. Balancing simulation accuracy and efficiency with the Amber united atom force field.
    Hsieh MJ, Luo R.
    J Phys Chem B; 2010 Mar 04; 114(8):2886-93. PubMed ID: 20131885
    [Abstract] [Full Text] [Related]

  • 3. 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]

  • 4. CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.
    Patel S, Mackerell AD, Brooks CL.
    J Comput Chem; 2004 Sep 16; 25(12):1504-14. PubMed ID: 15224394
    [Abstract] [Full Text] [Related]

  • 5. A coarse-grained protein-protein potential derived from an all-atom force field.
    Basdevant N, Borgis D, Ha-Duong T.
    J Phys Chem B; 2007 Aug 09; 111(31):9390-9. PubMed ID: 17616119
    [Abstract] [Full Text] [Related]

  • 6. Application of torsion angle molecular dynamics for efficient sampling of protein conformations.
    Chen J, Im W, Brooks CL.
    J Comput Chem; 2005 Nov 30; 26(15):1565-78. PubMed ID: 16145655
    [Abstract] [Full Text] [Related]

  • 7. The SAAP force field. A simple approach to a new all-atom protein force field by using single amino acid potential (SAAP) functions in various solvents.
    Iwaoka M, Tomoda S.
    J Comput Chem; 2003 Jul 30; 24(10):1192-200. PubMed ID: 12820126
    [Abstract] [Full Text] [Related]

  • 8. 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]

  • 9. Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution.
    Hu H, Elstner M, Hermans J.
    Proteins; 2003 Feb 15; 50(3):451-63. PubMed ID: 12557187
    [Abstract] [Full Text] [Related]

  • 10. 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]

  • 11. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.
    Mackerell AD, Feig M, Brooks CL.
    J Comput Chem; 2004 Aug 30; 25(11):1400-15. PubMed ID: 15185334
    [Abstract] [Full Text] [Related]

  • 12. Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation.
    Katagiri D, Fuji H, Neya S, Hoshino T.
    J Comput Chem; 2008 Sep 30; 29(12):1930-44. PubMed ID: 18366016
    [Abstract] [Full Text] [Related]

  • 13. Comparative study of generalized born models: Born radii and peptide folding.
    Zhu J, Alexov E, Honig B.
    J Phys Chem B; 2005 Feb 24; 109(7):3008-22. PubMed ID: 16851315
    [Abstract] [Full Text] [Related]

  • 14. 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]

  • 15. Peptide-TiO2 surface interaction in solution by ab initio and molecular dynamics simulations.
    Carravetta V, Monti S.
    J Phys Chem B; 2006 Mar 30; 110(12):6160-9. PubMed ID: 16553430
    [Abstract] [Full Text] [Related]

  • 16. All-atom level direct folding simulation of a betabetaalpha miniprotein.
    Jang S, Kim E, Pak Y.
    J Chem Phys; 2008 Mar 14; 128(10):105102. PubMed ID: 18345926
    [Abstract] [Full Text] [Related]

  • 17. Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field.
    Cao Z, Lin Z, Wang J, Liu H.
    J Comput Chem; 2009 Mar 14; 30(4):645-60. PubMed ID: 18780355
    [Abstract] [Full Text] [Related]

  • 18. Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model.
    Liu Y, Beveridge DL.
    Proteins; 2002 Jan 01; 46(1):128-46. PubMed ID: 11746709
    [Abstract] [Full Text] [Related]

  • 19. Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone.
    Murarka RK, Liwo A, Scheraga HA.
    J Chem Phys; 2007 Oct 21; 127(15):155103. PubMed ID: 17949219
    [Abstract] [Full Text] [Related]

  • 20. Conformational simulations of aqueous solvated alpha-conotoxin GI and its single disulfide analogues using a polarizable force field model.
    Jiang N, Ma J.
    J Phys Chem A; 2008 Oct 09; 112(40):9854-67. PubMed ID: 18788721
    [Abstract] [Full Text] [Related]

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