Table 1.
| Scoring functions | Descriptions |
|---|---|
| General scoring [9] |
A linear empirical scoring function can be written as a sum of independent terms such as ΔGbindig = c0 + c1 ΔGvdw + c2 ΔGhbond + c3 ΔGentropy where ci is the weighting coefficients of the respective ΔGbindig terms, adjusted to reproduce affinity data based on the training set. In the example, ΔGvdw is a Van der Waals potential, ΔGhbond is a specific term accounting for hydrogen bonds, and ΔGentropy is related to the ligand entropic loss upon binding |
| Surflex-score [11] | Surflex scoring function includes an entropic penalty term that is linear in the number of rotatable bonds in the ligand, intended to model the entropic cost of fixation of these bonds, and a term that is linearly related to the log of the molecular weight of the ligand, intended to generate putative poses of ligand fragments |
| G-score [12] | This scoring function is from GOLD program. It is basically a force field-based scoring function, which consists of terms for the hydrogen bonds and van der Waals interactions between protein and ligand and the internal steric energies of the ligand |
| PMF-score [13] | This knowledge-based scoring function was developed by Muegge et al. It sums up pairwise knowledge-based interaction potentials between protein and ligand |
| D-score [14] | This scoring function is adopted by the DOCK program by Kuntz et al., including Van der Waals and electrostatic interactions between protein and ligand |
| Chemscore [15] | This empirical scoring function is based on the work of Eldridge et al. which includes terms for hydrogen bonds, metal-ligand interactions, lipophilic contacts, and conformational entropies |