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Figure 2 | BMC Bioinformatics

Figure 2

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

Figure 2

Protonation of the ligand molecule by analysing the protein environment. Protonation of nitrogen atom N9 of molecule ADE339 depends on three parameters: the distance from ligand atom N9 to protein atom NH1 of ARG163, and the angles H-N9-NH1 and H1-NH1-N9. If hydrogen atoms H and H1 fall within a cone described by a solid angle of 60 degrees, then the hydrogen atom attached to the ligand ADE339 is removed (as indicated with a red X), even though the atom OE2 of GLU160 is in a favourable position to accept a hydrogen bond.

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BMC Bioinformatics

ISSN: 1471-2105

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