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Methods for Calculating the Entropy and Free Energy and their Application to Problems Involving Protein Flexibility and Ligand Binding

[ Vol. 10 , Issue. 3 ]

Author(s):

Hagai Meirovitch, Srinath Cheluvaraja and Ronald P. White   Pages 229 - 243 ( 15 )

Abstract:


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 and review recent methodological developments. Because protein flexibility is essential for function and ligand binding, we discuss the related problems involved in the definition, simulation, and free energy calculation of microstates (such as the α-helical region of a peptide). While the review is broad, a special emphasize is given to methods for calculating the absolute F (S), where our HSMC(D) method is described in some detail.

Keywords:

Helmholtz free energy, F, entropy, S, thermodynamic quantities, protein flexibility, ligand binding

Affiliation:

Department of Computational Biology, University of Pittsburgh School of Medicine, 3059 BST3, Pittsburgh, PA 15260, USA.



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