Table 3: Percentage of 1st 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
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

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