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Figure 3 | BMC Bioinformatics

Figure 3

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

Figure 3

Examples of molecules that were correctly protonated by the modified Babel program. A) Biotin. The atom C2 was correctly typed as sp3, and then a hydrogen was added to fill the empty valence; B) Moxiraprine. The hydrogen atoms marked with red X's were removed by applying an empirical rule that allows correct protonation of this type of ring.

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BMC Bioinformatics

ISSN: 1471-2105

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