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Journal Abstract Search


379 related items for PubMed ID: 15965971

  • 21. Geometry optimization based on linear response free energy with quantum mechanical/molecular mechanical method: applications to Menshutkin-type and Claisen rearrangement reactions in aqueous solution.
    Higashi M, Hayashi S, Kato S.
    J Chem Phys; 2007 Apr 14; 126(14):144503. PubMed ID: 17444719
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  • 22. Force field parameters for rotation around chi torsion axis in nucleic acids.
    Ode H, Matsuo Y, Neya S, Hoshino T.
    J Comput Chem; 2008 Nov 30; 29(15):2531-42. PubMed ID: 18470965
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  • 23. A combined QM/MM molecular dynamics simulations study of nitrate anion (NO3-) in aqueous solution.
    Tongraar A, Tangkawanwanit P, Rode BM.
    J Phys Chem A; 2006 Nov 30; 110(47):12918-26. PubMed ID: 17125309
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  • 24. 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
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  • 25. Are AM1 ligand-protein binding enthalpies good enough for use in the rational design of new drugs?
    Villar R, Gil MJ, García JI, Martínez-Merino V.
    J Comput Chem; 2005 Oct 16; 26(13):1347-58. PubMed ID: 16021597
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  • 26. Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding?
    Mitchell JB, Nandi CL, McDonald IK, Thornton JM, Price SL.
    J Mol Biol; 1994 Jun 03; 239(2):315-31. PubMed ID: 8196060
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  • 27. Computational study on the relative acidity of acetic acid by the QM/MM method combined with the theory of energy representation.
    Hori T, Takahashi H, Furukawa S, Nakano M, Yang W.
    J Phys Chem B; 2007 Jan 25; 111(3):581-8. PubMed ID: 17228916
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  • 28. 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
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  • 29. A study of N-methylacetamide in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics.
    Yang ZZ, Qian P.
    J Chem Phys; 2006 Aug 14; 125(6):64311. PubMed ID: 16942290
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  • 30. A combined effective fragment potential-fragment molecular orbital method. I. The energy expression and initial applications.
    Nagata T, Fedorov DG, Kitaura K, Gordon MS.
    J Chem Phys; 2009 Jul 14; 131(2):024101. PubMed ID: 19603964
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  • 31. Origin of intrinsic 3(10)-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field.
    Jagielska A, Skolnick J.
    J Comput Chem; 2007 Jul 30; 28(10):1648-57. PubMed ID: 17342701
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  • 32. New angle-dependent potential energy function for backbone-backbone hydrogen bond in protein-protein interactions.
    Choi H, Kang H, Park H.
    J Comput Chem; 2010 Apr 15; 31(5):897-903. PubMed ID: 19618414
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  • 33. QM-MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians.
    Geerke DP, Thiel S, Thiel W, van Gunsteren WF.
    Phys Chem Chem Phys; 2008 Jan 14; 10(2):297-302. PubMed ID: 18213415
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  • 34. QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study.
    Sinnecker S, Neese F.
    J Comput Chem; 2006 Sep 14; 27(12):1463-75. PubMed ID: 16807973
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  • 35. A multicore QM/MM approach for the geometry optimization of chromophore aggregate in protein.
    Kiyota Y, Hasegawa JY, Fujimoto K, Swerts B, Nakatsuji H.
    J Comput Chem; 2009 Jun 14; 30(8):1351-9. PubMed ID: 19009605
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  • 36. Electronic structure, binding energy, and solvation structure of the streptavidin-biotin supramolecular complex: ONIOM and 3D-RISM study.
    Li Q, Gusarov S, Evoy S, Kovalenko A.
    J Phys Chem B; 2009 Jul 23; 113(29):9958-67. PubMed ID: 19545155
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  • 37. Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: comparisons with IR and vibrational circular dichroism spectra.
    Kwac K, Lee KK, Han JB, Oh KI, Cho M.
    J Chem Phys; 2008 Mar 14; 128(10):105106. PubMed ID: 18345930
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  • 38. Theoretical investigation of CO interaction with copper sites in zeolites: periodic DFT and hybrid quantum mechanical/interatomic potential function study.
    Bludský O, Silhan M, Nachtigall P, Bucko T, Benco L, Hafner J.
    J Phys Chem B; 2005 May 19; 109(19):9631-8. PubMed ID: 16852159
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  • 39. Spectroscopically determined force field for water dimer: physically enhanced treatment of hydrogen bonding in molecular mechanics energy functions.
    Mannfors B, Palmo K, Krimm S.
    J Phys Chem A; 2008 Dec 11; 112(49):12667-78. PubMed ID: 19012387
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  • 40. Zinc binding in proteins and solution: a simple but accurate nonbonded representation.
    Stote RH, Karplus M.
    Proteins; 1995 Sep 11; 23(1):12-31. PubMed ID: 8539245
    [Abstract] [Full Text] [Related]


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