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567 related items for PubMed ID: 15521059

  • 1. Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics.
    De Mori GM, Colombo G, Micheletti C.
    Proteins; 2005 Feb 01; 58(2):459-71. PubMed ID: 15521059
    [Abstract] [Full Text] [Related]

  • 2. Contact pair dynamics during folding of two small proteins: chicken villin head piece and the Alzheimer protein beta-amyloid.
    Mukherjee A, Bagchi B.
    J Chem Phys; 2004 Jan 15; 120(3):1602-12. PubMed ID: 15268287
    [Abstract] [Full Text] [Related]

  • 3. Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations.
    Ulmschneider JP, Ulmschneider MB, Di Nola A.
    J Phys Chem B; 2006 Aug 24; 110(33):16733-42. PubMed ID: 16913813
    [Abstract] [Full Text] [Related]

  • 4. The folding pathway of ubiquitin from all-atom molecular dynamics simulations.
    Marianayagam NJ, Jackson SE.
    Biophys Chem; 2004 Oct 01; 111(2):159-71. PubMed ID: 15381313
    [Abstract] [Full Text] [Related]

  • 5. Coarse-grained protein model with residue orientation energies derived from atomic force fields.
    Betancourt MR.
    J Phys Chem B; 2009 Nov 05; 113(44):14824-30. PubMed ID: 19817469
    [Abstract] [Full Text] [Related]

  • 6. Monte Carlo simulation of protein folding in the presence of residue-specific binding sites.
    Rossinsky E, Srebnik S.
    Biopolymers; 2005 Dec 05; 79(5):259-68. PubMed ID: 16134169
    [Abstract] [Full Text] [Related]

  • 7. 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]

  • 8. A coarse-grained protein force field for folding and structure prediction.
    Maupetit J, Tuffery P, Derreumaux P.
    Proteins; 2007 Nov 01; 69(2):394-408. PubMed ID: 17600832
    [Abstract] [Full Text] [Related]

  • 9. A new Hybrid Monte Carlo algorithm for protein potential function test and structure refinement.
    Zhang H.
    Proteins; 1999 Mar 01; 34(4):464-71. PubMed ID: 10081959
    [Abstract] [Full Text] [Related]

  • 10. All-atom fast protein folding simulations: the villin headpiece.
    Shen MY, Freed KF.
    Proteins; 2002 Dec 01; 49(4):439-45. PubMed ID: 12402354
    [Abstract] [Full Text] [Related]

  • 11. Global optimization and folding pathways of selected alpha-helical proteins.
    Carr JM, Wales DJ.
    J Chem Phys; 2005 Dec 15; 123(23):234901. PubMed ID: 16392943
    [Abstract] [Full Text] [Related]

  • 12. Exploration of compact protein conformations using the guided replication Monte Carlo method.
    Solomon JE, Liney D.
    Biopolymers; 1995 Nov 15; 36(5):579-97. PubMed ID: 7578950
    [Abstract] [Full Text] [Related]

  • 13. All-atom Monte Carlo simulation of GCAA RNA folding.
    Nivón LG, Shakhnovich EI.
    J Mol Biol; 2004 Nov 12; 344(1):29-45. PubMed ID: 15504400
    [Abstract] [Full Text] [Related]

  • 14. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.
    Schueler-Furman O, Wang C, Baker D.
    Proteins; 2005 Aug 01; 60(2):187-94. PubMed ID: 15981249
    [Abstract] [Full Text] [Related]

  • 15. 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]

  • 16. Ab initio discrete molecular dynamics approach to protein folding and aggregation.
    Urbanc B, Borreguero JM, Cruz L, Stanley HE.
    Methods Enzymol; 2006 Dec 03; 412():314-38. PubMed ID: 17046666
    [Abstract] [Full Text] [Related]

  • 17. Coarse-grained protein molecular dynamics simulations.
    Derreumaux P, Mousseau N.
    J Chem Phys; 2007 Jan 14; 126(2):025101. PubMed ID: 17228975
    [Abstract] [Full Text] [Related]

  • 18. Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in beta-hairpins.
    Imamura H, Chen JZ.
    Proteins; 2006 May 15; 63(3):555-70. PubMed ID: 16485280
    [Abstract] [Full Text] [Related]

  • 19. Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?
    Zagrovic B, van Gunsteren WF.
    Proteins; 2006 Apr 01; 63(1):210-8. PubMed ID: 16425239
    [Abstract] [Full Text] [Related]

  • 20. Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece.
    Jayachandran G, Vishal V, Pande VS.
    J Chem Phys; 2006 Apr 28; 124(16):164902. PubMed ID: 16674165
    [Abstract] [Full Text] [Related]

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