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Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation.
  • H. Meirovitch
  • Chemistry, Medicine
  • Current opinion in structural biology
  • 1 April 2007
The Helmholtz free energy, F, plays an important role in proteins because of their rugged potential energy surface, which is 'decorated' with a tremendous number of local wells (denoted microstates,Expand
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The optimal fraction of hydrophobic residues required to ensure protein collapse.
The hydrophobic interaction is the main driving force for protein folding. Here, we address the question of what is the optimal fraction, f of hydrophobic (H) residues required to ensure proteinExpand
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Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding.
The Helmholtz free energy, F and the entropy, S are related thermodynamic quantities with a special importance in structural biology. We describe the difficulties in calculating these quantities andExpand
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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.Expand
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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)Expand
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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) = -20.4 kcal/mol. Therefore, this complex became a target for a large number ofExpand
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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 theirExpand
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The effect of loops on the structural organization of alpha-helical membrane proteins.
Loops connecting the transmembrane (TM) alpha-helices in membrane proteins are expected to affect the structural organization of the thereby connected helices and the helical bundles as a whole. ThisExpand
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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.Expand
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