Table 2: Percentage of top 10 scored intercalated decoys with an RMSD less than 2.0 Å and higher than 4.0 Å among the four docking algorithms and their associated scoring functions.

PDB code Percentage of decoys with RMSD <2.0 Å Percentage of decoys with RMSD >4.0 Å
ASP ChemScore GoldScore Autodock ASP ChemScore GoldScore Autodock
1l1h 10 0 20 50 40 100 20 40
2gb9 10 0 10 0 60 100 70 90
3ce5 0 0 0 0 30 80 50 100
3em2 0 0 10 30 50 100 40 50
3eqw 0 0 10 0 100 100 30 50
3eru 0 0 10 0 80 100 40 60
3es0 0 0 0 10 90 100 90 50
3et8 0 0 0 0 100 100 80 40
3eui 0 0 10 0 70 100 60 90
3eum 0 0 20 0 60 100 30 90
3nyp 10 0 0 0 80 70 30 50
3nz7 0 0 20 10 50 100 20 70
3qsc 0 0 0 0 100 100 100 100
3qsf 0 0 0 0 100 100 100 100
Mean 2.14 0.00 7.86 7.14 72.14 96.43 54.29 70.00

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