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Computer simulation of self-avoiding walks: Testing the scanning method
The scanning method is a computer simulation technique for macromolecules suggested recently. The method is described here in detail and its applicability (in contrast to other simulation techniques)
Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.
Because protein flexibility is essential for function and ligand binding, the related problems involved in the definition, simulation, and free energy calculation of microstates (such as the alpha-helical region of a peptide) are discussed.
Absolute free energy of binding of avidin/biotin, revisited.
The binding of biotin to avidin is one of the strongest in nature with absolute free energy of binding, ΔA(0), which is calculated here by rigorous statistical mechanical methods and models that consider long-range electrostatics.
Simulation of a free energy upper bound, based on the anticorrelation between an approximate free energy functional and its fluctuation
The local states and hypothetical scanning methods enable one to define a series of lower bound approximations for the free energy, FA from a sample of configurations simulated by any exact method.
A Simple and Effective Procedure for Conformational Search of Macromolecules: Application to Met- and Leu-Enkephalin
A simple and efficient method for searching the conformational space of macromolecules is presented. With this method an initial set of relatively low-energy structures is generated, and their
Collapse transition of self-avoiding walks on a square lattice in the bulk and near a linear wall : the universality classes of the θ and θ' points
Using the scanning method we study by extensive simulations the θ transition of self-avoiding walks with nearest-neighbor attractions in the bulk and near a linear wall on a square lattice.