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Conformational and translational-rotational entropy from molecular ensembles
1  University of Udine

Published: 05 May 2021 by MDPI in Entropy 2021: The Scientific Tool of the 21st Century session Thermodynamics

Entropy calculation is an important step in the postprocessing of molecular
dynamics trajectories or predictive models. In recent years the nearest
neighbor method proposed by Demchuk and coworkers [1] has emerged as a powerful
method to deal in a flexible way with the dimensionality of the problem.
Applications to most important biomolecular processes have been presented [2,3]
and a specific development has concerned the computation of
rotational-translational entropy which required in turn the definition of a
metric in rotation-translation space [4].
Two programs have been developed to compute conformational and
rotational-translational entropies from biomolecular ensembles [5].
Possible estensions of the method will be presented.

[1] Nearest neighbor estimates of entropy
H Singh, N Misra, V Hnizdo, A Fedorowicz, E Demchuk
American Journal of Mathematical and Management Sciences, 23 (3-4), 301-321,

[2] Free energy, enthalpy and entropy from implicit solvent end-point
F Fogolari, A Corazza, G Esposito
Frontiers in Molecular Biosciences 5, 11, 2018

[3] Distance-based configurational entropy of proteins from molecular dynamics
F Fogolari, A Corazza, S Fortuna, MA Soler, B VanSchouwen, G Brancolini, S
Corni, G Melacini, G Esposito
PLoS One 10 (7), 2015

[4] Accurate Estimation of the Entropy of Rotation-Translation Probability
F Fogolari, CJ Dongmo Foumthuim, S Fortuna, MA Soler, A Corazza, G Esposito
Journal of chemical theory and computation 12 (1), 1-8, 2016

[5] PDB2ENTROPY and PDB2TRENT: Conformational and Translational-Rotational
Entropy from Molecular Ensembles
F Fogolari, O Maloku, CJ Dongmo Foumthuim, A Corazza, G Esposito
Journal of chemical information and modeling 58 (7), 1319-1324, 2018

Keywords: conformational entropy; rotation-translation entropy