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Table 2 Statistics from the Babel 1.6 runs on the DOCK 4.0 dataset to test the protonation

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

Errors *

%

Nitrogen

85

41

48

Oxygen

128

0

0

Carbon

871

1

0.1

Others

30

0

0

Total

1114

42

3.7

  1. *) Number of atoms carrying a different protonation, as compared with the original dataset files.
  2. Errors in the protonation resulted either from an incorrect assignment of the hybridization or from an incorrect filling of a valence of a sp2 nitrogen in a ring structure.
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BMC Bioinformatics

ISSN: 1471-2105

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