Evaluation of Scoring Function Performance on DNA-ligand Complexes

Table 3: Percentage of 1^st ranked structure with RMSD less than 2.0 Å and higher than 4.0 Å among the four docking algorithms and their associated scoring functions.

DNA-ligand Complexes	Scoring Functions
DNA-ligand Complexes	ASP	ChemScore	GoldScore	Autodock
*RMSD <2.0 Å*
All	9.09	9.09	18.18	33.33
Minor groove	21.43	14.29	28.57	50.00
Intercalated	0.00	7.14	14.29	21.43
*RMSD >4.0 Å*
All	87.88	84.85	63.64	54.55
Minor groove	78.57	71.43	64.29	42.86
Intercalated	92.86	92.86	50.00	57.14