Daggett V, Levitt M. Realistic simulations of native-protein dynamics in solution and beyond. Annu Rev Biophys Biomol Struct 1993;22:353--380.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....clusters and polymers. 2. 3 Molecular Dynamics Molecular dynamics (MD) represents structural data along with physical interactions as empirically weighted energy terms in a force field and traces the conformational changes of the molecule using Newton s equations of motion (see for example [20, 24, 62, 67]) This method is commonly used to study the folding process of proteins but may also be used to refine a structure by allowing it to reach equilibrium. For several small molecules, MD under simulated annealing of temperature has been demonstrated to evolve the correct structure, even from random ....

....because the parallelism in the force summation within a time step may be limited. An important caution to take in a MD simulation is the appropriate assignment of weights for the energy terms in the force field, since the quality of the result can be greatly affected by it (see discussion in [24]) The energy parameters may need to be re tuned for a particular model of a molecule to get sensible results. When the force calculations contain energy terms representing structural constraints in addition to physical interactions, the computation is usually referred to as restrained molecular ....

V. Daggett and M. Levitt, "Realistic Simulations of Native-Protein Dynamics in Solution and Beyond", Annu. Rev. Biophys. Biomol. Struct., vol. 22, pp. 353-380, 1993.

....or the rates of association and dissociation. The two principal simulation techniques used are molecular dynamics and Monte Carlo simulation. Molecular dynamics attempts to simulate the true dynamics of a system using Newton s equations of motion [Anderson, 1980; McCammon, 1987; Haile, 1992; Daggett and Levitt, 1993; Leach and Klein, 1995] Monte Carlo methods use a randomized approach to generating successive ligand configurations and compute thermodynamic properties by averaging over all samples that were generated [Rubinstein, 1981; Knegtel et al. 1994; Cummings et al. 1995] While both molecular ....

Daggett, V. and Levitt, M. (1993). Realistic simulations of native-protein dynamics in solution and beyond. Annu Rev Biophys Biomol Struct, 22:353-80.

....or the rates of association and dissociation. The two principal simulation techniques used are molecular dynamics and Monte Carlo simulation. Molecular dynamics attempts to simulate the true dynamics of a system using Newton s equations of motion [Anderson, 1980; McCammon, 1987; Haile, 1992; Daggett and Levitt, 1993; Leach and Klein, 1995] Monte Carlo methods use a randomized approach to generating successive ligand configurations and compute thermodynamic properties by averaging over all samples that were generated [Rubinstein, 1981; Knegtel et al. 1994; Cummings et al. 1995] While both molecular ....

Daggett, V. and Levitt, M. (1993). Realistic simulations of native-protein dynamics in solution and beyond. Annu Rev Biophys Biomol Struct, 22:353-80.

....with experimental results to effectively describe the molecular system. A number of empirically based molecular mechanics models have been developed for protein systems, including AMBER [74, 187, 188] CHARMM [19] DISCOVER [37] ECEPP [121, 122, 123] ECEPP 2 [130] ECEPP 3 [131] ENCAD [36, 103], GROMOS [175] MM2 [7] and MM3 [8, 106, 107] These models, also known as force fields, are typically expressed as summations of several potential energy components, with the mathematical form of individual energy terms based on the phenomenological nature of that term. A general total energy ....

V. Daggett and M. Levitt, Realistic simulations of native-protein dynamics in solution and beyond, Annu. Rev. Biophys. Biomol. Struct., 22, (1993), 353-380.

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Daggett V, Levitt M. Realistic simulations of native-protein dynamics in solution and beyond. Annu Rev Biophys Biomol Struct 1993;22:353--380.

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Daggett, V. and M. Levitt, Realistic Simulations of Native-Protein Dynamics in Solution and Beyond. Ann. Rev. Biophys. Biomol. Struct., 1993. 22: p. 353-380.

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Daggett, V. & Levitt, M. (1993). Realistic simulations of native-protein dynamics in solution and beyond. Annu. Rev. Biophys. Biomol. Struct. 22, 353--380.

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