Conformational and translational-rotational entropy from molecular ensembles

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 entropyH Singh, N Misra, V Hnizdo, A Fedorowicz, E DemchukAmerican Journal of Mathematical and Management Sciences, 23 (3-4), 301-321, 2003 [2] Free energy, enthalpy and entropy from implicit solvent end-point simulationsF Fogolari, A Corazza, G EspositoFrontiers in Molecular Biosciences 5, 11, 2018 [3] Distance-based configurational entropy of proteins from molecular dynamics simulationsF Fogolari, A Corazza, S Fortuna, MA Soler, B VanSchouwen, G Brancolini, S Corni, G Melacini, G EspositoPLoS One 10 (7), 2015 [4] Accurate Estimation of the Entropy of Rotation-Translation Probability DistributionsF 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 EnsemblesF Fogolari, O Maloku, CJ Dongmo Foumthuim, A Corazza, G EspositoJournal of chemical information and modeling 58 (7), 1319-1324, 2018