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223 related items for PubMed ID: 16853098

  • 1. Modeling the interplay between geometrical and energetic effects in protein folding.
    Suzuki Y, Onuchic JN.
    J Phys Chem B; 2005 Sep 01; 109(34):16503-10. PubMed ID: 16853098
    [Abstract] [Full Text] [Related]

  • 2. An analytical study of the interplay between geometrical and energetic effects in protein folding.
    Suzuki Y, Noel JK, Onuchic JN.
    J Chem Phys; 2008 Jan 14; 128(2):025101. PubMed ID: 18205476
    [Abstract] [Full Text] [Related]

  • 3. Cooperativity in two-state protein folding kinetics.
    Weikl TR, Palassini M, Dill KA.
    Protein Sci; 2004 Mar 14; 13(3):822-9. PubMed ID: 14978313
    [Abstract] [Full Text] [Related]

  • 4. Molecular mechanisms for cooperative folding of proteins.
    Hao MH, Scheraga HA.
    J Mol Biol; 1998 Apr 10; 277(4):973-83. PubMed ID: 9545385
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  • 5. The effect of surface tethering on the folding of the src-SH3 protein domain.
    Zhuang Z, Jewett AI, Soto P, Shea JE.
    Phys Biol; 2009 Feb 10; 6(1):015004. PubMed ID: 19208934
    [Abstract] [Full Text] [Related]

  • 6. Probing possible downhill folding: native contact topology likely places a significant constraint on the folding cooperativity of proteins with approximately 40 residues.
    Badasyan A, Liu Z, Chan HS.
    J Mol Biol; 2008 Dec 12; 384(2):512-30. PubMed ID: 18823994
    [Abstract] [Full Text] [Related]

  • 7. Folding pathway dependence on energetic frustration and interaction heterogeneity for a three-dimensional hydrophobic protein model.
    Garcia LG, Araújo AF.
    Proteins; 2006 Jan 01; 62(1):46-63. PubMed ID: 16292745
    [Abstract] [Full Text] [Related]

  • 8. Geometrical features of the protein folding mechanism are a robust property of the energy landscape: a detailed investigation of several reduced models.
    Oliveira LC, Schug A, Onuchic JN.
    J Phys Chem B; 2008 May 15; 112(19):6131-6. PubMed ID: 18251535
    [Abstract] [Full Text] [Related]

  • 9. Folding of a SH3 domain: standard and "hydrodynamic" analyses.
    Kalgin IV, Karplus M, Chekmarev SF.
    J Phys Chem B; 2009 Sep 24; 113(38):12759-72. PubMed ID: 19711956
    [Abstract] [Full Text] [Related]

  • 10. Roles of physical interactions in determining protein-folding mechanisms: molecular simulation of protein G and alpha spectrin SH3.
    Lee SY, Fujitsuka Y, Kim DH, Takada S.
    Proteins; 2004 Apr 01; 55(1):128-38. PubMed ID: 14997547
    [Abstract] [Full Text] [Related]

  • 11. Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations.
    Ding F, Guo W, Dokholyan NV, Shakhnovich EI, Shea JE.
    J Mol Biol; 2005 Jul 29; 350(5):1035-50. PubMed ID: 15982666
    [Abstract] [Full Text] [Related]

  • 12. Robustness and generalization of structure-based models for protein folding and function.
    Lammert H, Schug A, Onuchic JN.
    Proteins; 2009 Dec 29; 77(4):881-91. PubMed ID: 19626713
    [Abstract] [Full Text] [Related]

  • 13. Multidimensional theory of protein folding.
    Itoh K, Sasai M.
    J Chem Phys; 2009 Apr 14; 130(14):145104. PubMed ID: 19368477
    [Abstract] [Full Text] [Related]

  • 14. Transition states for folding of circular-permuted proteins.
    Chen J, Wang J, Wang W.
    Proteins; 2004 Oct 01; 57(1):153-71. PubMed ID: 15326601
    [Abstract] [Full Text] [Related]

  • 15. Entropy capacity determines protein folding.
    Galzitskaya OV, Garbuzynskiy SO.
    Proteins; 2006 Apr 01; 63(1):144-54. PubMed ID: 16400647
    [Abstract] [Full Text] [Related]

  • 16. Parallel folding pathways in the SH3 domain protein.
    Lam AR, Borreguero JM, Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich E.
    J Mol Biol; 2007 Nov 09; 373(5):1348-60. PubMed ID: 17900612
    [Abstract] [Full Text] [Related]

  • 17. Thermodynamics of binding to SH3 domains: the energetic impact of polyproline II (PII) helix formation.
    Ferreon JC, Hilser VJ.
    Biochemistry; 2004 Jun 22; 43(24):7787-97. PubMed ID: 15196021
    [Abstract] [Full Text] [Related]

  • 18. Computational protein design with side-chain conformational entropy.
    Sciretti D, Bruscolini P, Pelizzola A, Pretti M, Jaramillo A.
    Proteins; 2009 Jan 22; 74(1):176-91. PubMed ID: 18618711
    [Abstract] [Full Text] [Related]

  • 19. Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics.
    Borreguero JM, Dokholyan NV, Buldyrev SV, Shakhnovich EI, Stanley HE.
    J Mol Biol; 2002 May 03; 318(3):863-76. PubMed ID: 12054829
    [Abstract] [Full Text] [Related]

  • 20. Calculation of protein heat capacity from replica-exchange molecular dynamics simulations with different implicit solvent models.
    Yeh IC, Lee MS, Olson MA.
    J Phys Chem B; 2008 Nov 27; 112(47):15064-73. PubMed ID: 18959439
    [Abstract] [Full Text] [Related]

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