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With a number of simple approximations, MM/PBSA and LIE can provide relatively good binding affinity at a moderate computational cost. MM/PBSA approximates binding affinities combining molecular mechanics and continuum solvent approaches with difficulty, however, to predict the entropic contribution to the binding affinity. LIE is a semi-empirical MD approach which 46 New Developments in Medicinal Chemistry, Vol. 2 Taft et al. assumes that the binding affinity can be extracted from simulations of the free and bound states of the ligand whereas, however, two MD simulations are needed, one for the complex and the other for free ligand in water.

Recent work suggest improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization. The authors use minimization, MD, MM/PBSA and their incorporated specific charge model (PPC) to obtain correct ranking of binding poses in which bridging water molecules and electronic polarization play an important role [553]. Recent studies report optimization of molecular docking scores with ‘support vector rank regression’ (SVM), a statistical learning strategy that in principle represents a major advance in machine leaning methodology [554].

In these methods, a dielectric 48 New Developments in Medicinal Chemistry, Vol. 2 Taft et al. continuum solvent assumed outside a cavity is constructed around the solute molecule. The polarization of the continuum screens the electric field arising from nuclei and electron distribution. The surface charge density on the boundary represents the effects of polarization. The entire effect of dielectric polarization is described by screening charges arising on the interface. Cavity surface and solute describe the local system (problem) [578].

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