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. 2007 Aug 25;8:310. doi: 10.1186/1471-2105-8-310

Figure 3.

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.