title: Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation.
abstract: 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, m). F governs protein folding, whereas differences DeltaF(mn) determine the relative populations of microstates that are visited by a flexible cyclic peptide or a flexible protein segment (e.g. a surface loop). Recently developed methodologies for calculating DeltaF(mn) (and entropy differences, DeltaS(mn)) mainly use thermodynamic integration and calculation of the absolute F; interesting new approaches in these categories are the adaptive integration method and the hypothetical scanning molecular dynamics method, respectively.
authors: Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA. hagaim@pitt.edu
authors: Hagai
authors: H
authors: Meirovitch
mesh_terms: D003198:Computer Simulation; D019277:Entropy; D008954:Models, Biological; D046912:Multiprotein Complexes / Q000737:chemistry; D017510:Protein Folding; D049490:Systems Biology; D013816:Thermodynamics
chemical_list: D046912:Multiprotein Complexes