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,
2003

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

[3] Distance-based configurational entropy of proteins from molecular dynamics
simulations
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
Distributions
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