Skip to main content

Table 3 Errors in atom typing/protonation process with FlexX-200 dataset, for the original and modified versions of the Babel 1.6 program

From: Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms

Chemical element

Number of atoms

Babel (original)

Babel (modified)

  

Errors

%

Errors

%

Nitrogen

431

54

12.5

34

7.8

Oxygen

1036

4

0.3

0

0

Carbon

2979

40

1.3

0

0

Others

120

1

0.8

0

0

Total

4566

99

2.2

34

0.7