Average Binding Energy

The average binding energy was proposed (Andrews, Craik et al, 1984) to measure the free energy of interaction that a small organic molecule might be expected to express in an interaction with a biological macromolecule.

Average binding energy is is calculated by summing the intrinsic binding energies of specific functional groups present in the molecule and subtracting an entropic factor (T∆S= -14kcal/mol) and a term related to the degrees of internal rotational degrees of freedom (-.7).

The intrinsic binding energies were calculated for 10 functional groups by regression analysis applied on a training set of 200 drug molecules. Compounds can then be sorted on the basis of the binding energy values, the higher the binding energy of a compound the higher is its druglikeness.

We are going to use rdkit to make the average binding energy prediction. The program will loop through each of the molecules in the dataset and create a score. This is a rough measure of druglikeness. The higher the average binding score, the more druglike a compound is. This requires someone has python and rdkit installed.

from rdkit import Chem
from rdkit.Chem import Descriptors
import pandas as pd

single = ‘CC’
double = ‘C=C’
nsingle= ‘N’
nplus= ‘[N+]’
hydroxyl= ‘O[H]’…