Editing ChargeCalculator:Motivation (section)

=Generating molecular conformations=

The energy and properties of a molecular system depend on the 3D molecular structure. In order to predict the binding properties of a ligand to a target (e.g., before the synthesis of a potential drug candidate) it is necessary to have information about the possible conformations of the ligand at the given active site. Such information can be obtained by modeling techniques (docking, molecular dynamics, etc.). However, reaching a suitable ligand conformation from an initial state which is very different from a conformation that binds successfully can be very demanding computationally. To ensure that plausible conformations are sampled, it is often useful to start with several different conformations of the ligand. 

Many tools have been developed for the generation of different molecular conformers. These tools employ various heuristics for the generation of thousands of conformations for a single ligand molecule, and then evaluate the energy of each conformation. Atomic charges are often used in the estimation of the electrostatic contribution to the total energy of each particular conformation.