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Updated: Jul 16, 2026

New Features in Visual Dynamics 3.0
Published on: August 9, 2024
Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer
1Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA. hagaim@pitt.edu
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.
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