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of special interest. By treating the coupling variable in free energy simulations as a dynamic variable, the authors are able to increase the efficiency of a variety of free energy calculations.
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Kong X, Brooks CL. Lambda-dynamics: a new approach to free energy calculations. of special interest J Chem Phys. 105:1996;2414-2423 By treating the coupling variable in free energy simulations as a dynamic variable, the authors are able to increase the efficiency of a variety of free energy calculations.
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of special interest. This paper provides valuable insight and useful formulas for correcting the results of free energy simulations that involve changes in the internal coordinates that are subject to constraints.
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of special interest. The authors introduce the use of grand ensemble sampling to add or remove water molecules from binding pockets in calculations of free energies of binding.
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Resat H, Marrone TJ, McCammon JA. Enzyme-inhibitor association thermodynamics: explicit and continuum solvent studies. of special interest Biophys J. 72:1997;522-532 The authors introduce the use of grand ensemble sampling to add or remove water molecules from binding pockets in calculations of free energies of binding.
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Biophys J
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of special interest. This is a very useful review of the molecular dynamics method for sampling configurations, including the use of larger time steps to increase sampling efficiency.
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Schlick T, Barth E, Mandziuk M. Biomolecular dynamics at long timesteps: bridging the timescale gap between simulation and experimentation. of special interest Annu Rev Biophys Biomol Struct. 26:1997;181-222 This is a very useful review of the molecular dynamics method for sampling configurations, including the use of larger time steps to increase sampling efficiency.
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The low dielectric interior of proteins is sufficient to cause major structural changes in DNA on association
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of special interest. The binding of many biomolecular pairs involves sizable deformations of one or both molecules. This paper demonstrates that molecular dynamics simulations with continuum solvent models can rapidly generate such deformations. This is likely to prove useful in future simulations of the docking of flexible biomolecules.
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Simulation of the diffusional association of barnase and barstar
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of outstanding interest. This paper makes use of several innovations to provide an important new Brownian dynamics approach for calculating rates of protein - protein binding. Effective charges are used to approximate the effect of the low dielectric volumes of the proteins on their electrostatic interaction, and a valuable analysis of the criteria for successful binding is presented.
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Gabdoulline RR, Wade RC. Simulation of the diffusional association of barnase and barstar. of outstanding interest Biophys J. 72:1997;1917-1929 This paper makes use of several innovations to provide an important new Brownian dynamics approach for calculating rates of protein - protein binding. Effective charges are used to approximate the effect of the low dielectric volumes of the proteins on their electrostatic interaction, and a valuable analysis of the criteria for successful binding is presented.
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Biophys J
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41
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Weighted-ensemble Brownian dynamics simulations for protein association reactions
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of outstanding interest. The authors describe a novel way of generating the trajectory statistics needed for rate constant calculations by Brownian dynamics simulation. The method involves eliminating certain members of the ensemble of diffusing reactant pairs, and duplicating others, so as to insure adequate sampling of low probability configurations.
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Huber GA, Kim S. Weighted-ensemble Brownian dynamics simulations for protein association reactions. of outstanding interest Biophys J. 70:1996;97-110 The authors describe a novel way of generating the trajectory statistics needed for rate constant calculations by Brownian dynamics simulation. The method involves eliminating certain members of the ensemble of diffusing reactant pairs, and duplicating others, so as to insure adequate sampling of low probability configurations.
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Biophys J
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On the calculation of binding free energies using continuum methods: Application to MHC class I protein - Peptide interactions
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