Conformational Ensemble Profiles

The third step is to estimate the —> Conformational Ensemble Profile (GEP) for each compound by molecular dynamic simulation this profile encodes those conformations selected on the basis of the Boltzmann distribution. Then, different alignments are selected to compare the molecules of the training set. In the following step, each conformation of a molecule is placed in the reference grid space on the basis of the alignment scheme being explored and the thermodynamic probability of each grid cell occupied by each I PE type is computed. 

The growing computahonal power available to researchers proves an invaluable tool to investigate the dynamic profile of molecules. Molecular dynamics (MD) and Monte Carlo (MC) simulahons have thus become pivotal techniques to explore the dynamic dimension of physicochemical properhes [1]. Furthermore, the powerful computational methods based in parhcular on MIFs [7-10] allow some physicochemical properhes to be computed for each conformer (e.g. virtual log P), suggesting that to the conformahonal space there must correspond a property space covering the ensemble of all possible conformer-dependent property values. 

Within the mean-field approach to the many-molecule problem, the free energy is represented by considering an ensemble of independent molecules in an effeaive external field density profile as in the real system of interest. The problem is thus reduced to that of a single ideal (maao)molecule in a complex external mean field, which characterizes the many-body effects of the other (macro)molecules. Physically, this self-consistent calculation means that the molecular conformations are assumed to be in local equilibrium under the given density profiles (r). 

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