  This work examines the impact of energy over-minimization on an ensemble of
biological molecules subjected to the potential energy minimization procedure
in vacuum. In the studied structures, long potential energy minimization stage
leads to an increase of the main- and side-chain entropies in proteins. We show
that such over-minimization may diverge the protein structures from the
near-native attraction basin which possesses a minimum of free energy. We
propose a measure based on the Pareto front of total entropy for quality
assessment of minimized protein conformation. This measure may help in
selection of adequate number of energy minimization steps in protein modelling
and, thus, in preservation of the near-native protein conformation.
