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1861 related items for PubMed ID: 18959439

  • 1. 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]

  • 2. Free energy landscape of protein folding in water: explicit vs. implicit solvent.
    Zhou R.
    Proteins; 2003 Nov 01; 53(2):148-61. PubMed ID: 14517967
    [Abstract] [Full Text] [Related]

  • 3. Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.
    Olson MA, Feig M, Brooks CL.
    J Comput Chem; 2008 Apr 15; 29(5):820-31. PubMed ID: 17876760
    [Abstract] [Full Text] [Related]

  • 4. Probing the free energy landscape of the FBP28WW domain using multiple techniques.
    Periole X, Allen LR, Tamiola K, Mark AE, Paci E.
    J Comput Chem; 2009 May 15; 30(7):1059-68. PubMed ID: 18942730
    [Abstract] [Full Text] [Related]

  • 5. 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]

  • 6. The nature of the free energy barriers to two-state folding.
    Akmal A, Muñoz V.
    Proteins; 2004 Oct 01; 57(1):142-52. PubMed ID: 15326600
    [Abstract] [Full Text] [Related]

  • 7. Energy landscape of the trpzip2 peptide.
    Nymeyer H.
    J Phys Chem B; 2009 Jun 18; 113(24):8288-95. PubMed ID: 19469524
    [Abstract] [Full Text] [Related]

  • 8. Refinement of NMR structures using implicit solvent and advanced sampling techniques.
    Chen J, Im W, Brooks CL.
    J Am Chem Soc; 2004 Dec 15; 126(49):16038-47. PubMed ID: 15584737
    [Abstract] [Full Text] [Related]

  • 9. Coarse-grained lattice model simulations of sequence-structure fitness of a ribosome-inactivating protein.
    Olson MA, Yeh IC, Lee MS.
    Biopolymers; 2008 Feb 15; 89(2):153-9. PubMed ID: 17985366
    [Abstract] [Full Text] [Related]

  • 10. Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model.
    Felts AK, Harano Y, Gallicchio E, Levy RM.
    Proteins; 2004 Aug 01; 56(2):310-21. PubMed ID: 15211514
    [Abstract] [Full Text] [Related]

  • 11. Modeling loop reorganization free energies of acetylcholinesterase: a comparison of explicit and implicit solvent models.
    Olson MA.
    Proteins; 2004 Dec 01; 57(4):645-50. PubMed ID: 15481087
    [Abstract] [Full Text] [Related]

  • 12. Calculation of absolute ligand binding free energy to a ribosome-targeting protein as a function of solvent model.
    Lee MS, Olson MA.
    J Phys Chem B; 2008 Oct 23; 112(42):13411-7. PubMed ID: 18821791
    [Abstract] [Full Text] [Related]

  • 13. Thermodynamics and folding pathways of trpzip2: an accelerated molecular dynamics simulation study.
    Yang L, Shao Q, Gao YQ.
    J Phys Chem B; 2009 Jan 22; 113(3):803-8. PubMed ID: 19113829
    [Abstract] [Full Text] [Related]

  • 14. Is protein unfolding the reverse of protein folding? A lattice simulation analysis.
    Dinner AR, Karplus M.
    J Mol Biol; 1999 Sep 17; 292(2):403-19. PubMed ID: 10493884
    [Abstract] [Full Text] [Related]

  • 15. 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]

  • 16. Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations.
    Kannan S, Zacharias M.
    Proteins; 2009 Aug 01; 76(2):448-60. PubMed ID: 19173315
    [Abstract] [Full Text] [Related]

  • 17. Thermodynamic analysis of alpha-spectrin SH3 and two of its circular permutants with different loop lengths: discerning the reasons for rapid folding in proteins.
    Martínez JC, Viguera AR, Berisio R, Wilmanns M, Mateo PL, Filimonov VV, Serrano L.
    Biochemistry; 1999 Jan 12; 38(2):549-59. PubMed ID: 9888794
    [Abstract] [Full Text] [Related]

  • 18. Factors governing the foldability of proteins.
    Klimov DK, Thirumalai D.
    Proteins; 1996 Dec 12; 26(4):411-41. PubMed ID: 8990496
    [Abstract] [Full Text] [Related]

  • 19. Ab initio folding of helix bundle proteins using molecular dynamics simulations.
    Jang S, Kim E, Shin S, Pak Y.
    J Am Chem Soc; 2003 Dec 03; 125(48):14841-6. PubMed ID: 14640661
    [Abstract] [Full Text] [Related]

  • 20. Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water.
    Paschek D, Nymeyer H, García AE.
    J Struct Biol; 2007 Mar 03; 157(3):524-33. PubMed ID: 17293125
    [Abstract] [Full Text] [Related]

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