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Journal Abstract Search

165 related items for PubMed ID: 36379798

  • 21. Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent.
    Periole X, Mark AE.
    J Chem Phys; 2007 Jan 07; 126(1):014903. PubMed ID: 17212515
    [Abstract] [Full Text] [Related]

  • 22. Fundamental Redesign of the TIGER2hs Kernel to Address Severe Parameter Sensitivity.
    Schulig L, Geist N, Delcea M, Link A, Kulke M.
    J Chem Inf Model; 2022 Sep 12; 62(17):4200-4209. PubMed ID: 36004729
    [Abstract] [Full Text] [Related]

  • 23. An improved replica-exchange sampling method: temperature intervals with global energy reassignment.
    Li X, O'Brien CP, Collier G, Vellore NA, Wang F, Latour RA, Bruce DA, Stuart SJ.
    J Chem Phys; 2007 Oct 28; 127(16):164116. PubMed ID: 17979328
    [Abstract] [Full Text] [Related]

  • 24. All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permutation and Nonequilibrium Simulations.
    Itoh SG, Okumura H.
    Methods Mol Biol; 2022 Oct 28; 2340():197-220. PubMed ID: 35167076
    [Abstract] [Full Text] [Related]

  • 25. MuSTAR MD: multi-scale sampling using temperature accelerated and replica exchange molecular dynamics.
    Yamamori Y, Kitao A.
    J Chem Phys; 2013 Oct 14; 139(14):145105. PubMed ID: 24116651
    [Abstract] [Full Text] [Related]

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  • 27. Influence of various parameters in the replica-exchange molecular dynamics method: Number of replicas, replica-exchange frequency, and thermostat coupling time constant.
    Iwai R, Kasahara K, Takahashi T.
    Biophys Physicobiol; 2018 Oct 14; 15():165-172. PubMed ID: 30250775
    [Abstract] [Full Text] [Related]

  • 28. Exploring Conformational Change of Adenylate Kinase by Replica Exchange Molecular Dynamic Simulation.
    Wang J, Peng C, Yu Y, Chen Z, Xu Z, Cai T, Shao Q, Shi J, Zhu W.
    Biophys J; 2020 Mar 10; 118(5):1009-1018. PubMed ID: 31995738
    [Abstract] [Full Text] [Related]

  • 29. Increasing the Sampling Efficiency of Protein Conformational Change by Combining a Modified Replica Exchange Molecular Dynamics and Normal Mode Analysis.
    Peng C, Wang J, Shi Y, Xu Z, Zhu W.
    J Chem Theory Comput; 2021 Jan 12; 17(1):13-28. PubMed ID: 33351613
    [Abstract] [Full Text] [Related]

  • 30. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations.
    Jiang W, Roux B.
    J Chem Theory Comput; 2010 Jul 01; 6(9):2559-2565. PubMed ID: 21857813
    [Abstract] [Full Text] [Related]

  • 31. Recipes for free energy calculations in biomolecular systems.
    Moradi M, Babin V, Sagui C, Roland C.
    Methods Mol Biol; 2013 Jul 01; 924():313-37. PubMed ID: 23034754
    [Abstract] [Full Text] [Related]

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  • 33. Practical Protocols for Efficient Sampling of Kinase-Inhibitor Binding Pathways Using Two-Dimensional Replica-Exchange Molecular Dynamics.
    Shinobu A, Re S, Sugita Y.
    Front Mol Biosci; 2022 Jul 01; 9():878830. PubMed ID: 35573746
    [Abstract] [Full Text] [Related]

  • 34. Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.
    Zhang BW, Dai W, Gallicchio E, He P, Xia J, Tan Z, Levy RM.
    J Phys Chem B; 2016 Aug 25; 120(33):8289-301. PubMed ID: 27079355
    [Abstract] [Full Text] [Related]

  • 35. Multidimensional Replica Exchange Simulations for Efficient Constant pH and Redox Potential Molecular Dynamics.
    Cruzeiro VWD, Roitberg AE.
    J Chem Theory Comput; 2019 Feb 12; 15(2):871-881. PubMed ID: 30615455
    [Abstract] [Full Text] [Related]

  • 36. How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach.
    Nymeyer H.
    J Chem Theory Comput; 2008 Apr 12; 4(4):626-36. PubMed ID: 26620937
    [Abstract] [Full Text] [Related]

  • 37. The temperature intervals with global exchange of replicas empirical accelerated sampling method: parameter sensitivity and extension to a complex molecular system.
    Li X, Latour RA.
    J Comput Chem; 2011 Apr 30; 32(6):1091-100. PubMed ID: 20949510
    [Abstract] [Full Text] [Related]

  • 38. Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.
    Mishra SK, Kara M, Zacharias M, Koca J.
    Glycobiology; 2014 Jan 30; 24(1):70-84. PubMed ID: 24134878
    [Abstract] [Full Text] [Related]

  • 39. Hamiltonian replica exchange molecular dynamics using soft-core interactions.
    Hritz J, Oostenbrink C.
    J Chem Phys; 2008 Apr 14; 128(14):144121. PubMed ID: 18412437
    [Abstract] [Full Text] [Related]

  • 40. Replica exchange simulation method using temperature and solvent viscosity.
    Nguyen PH.
    J Chem Phys; 2010 Apr 14; 132(14):144109. PubMed ID: 20405987
    [Abstract] [Full Text] [Related]

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