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253 related items for PubMed ID: 16375567

  • 1. Efficient Monte Carlo trial moves for polypeptide simulations.
    Betancourt MR.
    J Chem Phys; 2005 Nov 01; 123(17):174905. PubMed ID: 16375567
    [Abstract] [Full Text] [Related]

  • 2. 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]

  • 3. Efficient chain moves for Monte Carlo simulations of a wormlike DNA model: excluded volume, supercoils, site juxtapositions, knots, and comparisons with random-flight and lattice models.
    Liu Z, Chan HS.
    J Chem Phys; 2008 Apr 14; 128(14):145104. PubMed ID: 18412482
    [Abstract] [Full Text] [Related]

  • 4. Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles.
    Whitelam S, Geissler PL.
    J Chem Phys; 2007 Oct 21; 127(15):154101. PubMed ID: 17949126
    [Abstract] [Full Text] [Related]

  • 5. Local moves: an efficient algorithm for simulation of protein folding.
    Elofsson A, Le Grand SM, Eisenberg D.
    Proteins; 1995 Sep 21; 23(1):73-82. PubMed ID: 8539252
    [Abstract] [Full Text] [Related]

  • 6. 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]

  • 7. Optimization of Monte Carlo trial moves for protein simulations.
    Betancourt MR.
    J Chem Phys; 2011 Jan 07; 134(1):014104. PubMed ID: 21218994
    [Abstract] [Full Text] [Related]

  • 8. Overcoming entropic barrier with coupled sampling at dual resolutions.
    Lwin TZ, Luo R.
    J Chem Phys; 2005 Nov 15; 123(19):194904. PubMed ID: 16321110
    [Abstract] [Full Text] [Related]

  • 9. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins.
    Abagyan R, Totrov M.
    J Mol Biol; 1994 Jan 21; 235(3):983-1002. PubMed ID: 8289329
    [Abstract] [Full Text] [Related]

  • 10. Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.
    Okumura H.
    J Chem Phys; 2008 Sep 28; 129(12):124116. PubMed ID: 19045015
    [Abstract] [Full Text] [Related]

  • 11. Dihedral angle principal component analysis of molecular dynamics simulations.
    Altis A, Nguyen PH, Hegger R, Stock G.
    J Chem Phys; 2007 Jun 28; 126(24):244111. PubMed ID: 17614541
    [Abstract] [Full Text] [Related]

  • 12. Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: chain breakage/closure algorithm and associated Jacobians.
    Sklenar H, Wüstner D, Rohs R.
    J Comput Chem; 2006 Feb 28; 27(3):309-15. PubMed ID: 16355439
    [Abstract] [Full Text] [Related]

  • 13. Solvent-shift Monte Carlo: a cluster algorithm for solvated systems.
    Hixson CA, Benigni JP, Earl DJ.
    Phys Chem Chem Phys; 2009 Aug 14; 11(30):6335-8. PubMed ID: 19809663
    [Abstract] [Full Text] [Related]

  • 14. Monte Carlo simulation and molecular theory of tethered polyelectrolytes.
    Hehmeyer OJ, Arya G, Panagiotopoulos AZ, Szleifer I.
    J Chem Phys; 2007 Jun 28; 126(24):244902. PubMed ID: 17614585
    [Abstract] [Full Text] [Related]

  • 15. Estimation of protein folding probability from equilibrium simulations.
    Rao F, Settanni G, Guarnera E, Caflisch A.
    J Chem Phys; 2005 May 08; 122(18):184901. PubMed ID: 15918759
    [Abstract] [Full Text] [Related]

  • 16. 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]

  • 17. Fast protein structure prediction using Monte Carlo simulations with modal moves.
    Carnevali P, Tóth G, Toubassi G, Meshkat SN.
    J Am Chem Soc; 2003 Nov 26; 125(47):14244-5. PubMed ID: 14624550
    [Abstract] [Full Text] [Related]

  • 18. Calculation of the entropy and free energy by the hypothetical scanning Monte Carlo method: application to peptides.
    Cheluvaraja S, Meirovitch H.
    J Chem Phys; 2005 Feb 01; 122(5):54903. PubMed ID: 15740349
    [Abstract] [Full Text] [Related]

  • 19. Knowledge-based potential for the polypeptide backbone.
    Betancourt MR.
    J Phys Chem B; 2008 Apr 24; 112(16):5058-69. PubMed ID: 18373361
    [Abstract] [Full Text] [Related]

  • 20. Folding of small proteins using a single continuous potential.
    Kim SY, Lee J, Lee J.
    J Chem Phys; 2004 May 01; 120(17):8271-6. PubMed ID: 15267747
    [Abstract] [Full Text] [Related]

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