Table 2.

Examples of scoring function formulae

Scoring function formulae	Ref.
$V=W_{vdw}\sum _{i,j}\left(\frac{A_{ij}}{r_{ij}^{12}}-\frac{B_{ij}}{r_{ij}^6}\right)+W_{hbond}\sum _{i,j}E\left(t\right)\left(\frac{C_{ij}}{r_{ij}^{12}}-\frac{D_{ij}}{r_{ij}^{10}}\right)+W_{elec}\sum _{i,j}\frac{q_i{q}_j}{∊\left(r_{ij}\right)r_{ij}}+W_{sol}\sum _{i,j}(S_i{V}_j+S_j{V}_i)e^{(-r_{ij}^2∕2{\sigma }^2)}$	[31]
Extended force-field-based scoring function from AutoDock.
For two atoms i, j, the pair-wise atomic energy is evaluated by the sum of van der Waals, hydrogen bond, coulomb energy and desolvation. W are weighted factors for calibrate the empirical free energy.
$\Delta G=\Delta G_0+\Delta G_{rot}\times N_{rot}+\Delta G_{hb}\sum _{neutralH-bond}f(\Delta R,\Delta \alpha )+\Delta G_{io}\sum _{ioninit.}f(\Delta R,\Delta \alpha )+\Delta G_{aro}\sum _{aroint.}f(\Delta R,\Delta \alpha )+\Delta G_{lipo}\sum _{lipocont.}{f}^{\ast }\left(\Delta R\right)$	[30]
Empirical scoring function from FlexX.
ΔG is the estimated free energy of binding; ΔG0 is the regression constant; ΔGrot , ΔGhb , ΔGio , ΔGaro and ΔGlipo are regression coefficients for each corresponding free energy term; f (ΔR,Δα) is scaling function penalizing deviations from the ideal geometry; Nrot is the number of free rotate bonds that are immobilized in the complex.
$PM\_score=\sum _{\underset{r<r_{cut-off}^{ij}}{kI}}{A}_{ij}\left(r\right)A_{ij}\left(r\right)=-k_{B}T\text{ln}\left[f_{Vol\_corr}^j\left(r\right)\frac{{\rho }_{seg}^{ij}\left(r\right)}{{\rho }_{bulk}^{ij}}\right]$	[84]
Knowledge-based scoring functions PMF.
kB is the Boltzmann constant; T is the absolute temperature; r is the atom pair distance. $f_{Vol\_corr}^j\left(r\right)$ is the ligand volume correction factor; $\frac{{\rho }_{seg}^{ij}\left(r\right)}{{\rho }_{bulk}^{ij}}$ designates the radial distribution function of a protein atom of type i and a ligand atom of type j.