Computational approaches like docking of the small ligand molecules into
large molecular targets and then to score their complementarily to
binding sites are used extensively in drug discovery. The number of
docking/scoring functions are increasing rapidly that use different
scoring and sampling algorithms. The effectiveness of such approaches
entirely depends upon reliable scoring function. Comparative studies are
needed to evaluate their current capabilities. This study was conducted
to analyze the effectiveness of MOE (MOLECULAR OPERATING ENVIRONMENT) in
docking of small ligand molecules and decoys to macromolecular protein
targets using force field, without using force field and Proxy triangle
scoring functions. It was found that using force field scoring function
showed a significant correlation between binding affinities predicted
scores of the docked complex. Using this approach correct binding mode
was identified with highest scoring among sampled poses. It was clear
from the results that selecting a suitable scoring function is crucial
for the evaluation of docking algorithm. The selection of scoring
function is dependent on the selected target.