Table 4

Excerpt of the background knowledge for protein 1BDG in Prolog
center_coords(p1BDG, p(27.0,22.1,64.9)).
has_aminoacid(p1BDG, a64, phe).
has_aminoacid(p1BDG, a85, leu).
has_aminoacid(p1BDG, a86, gly).
has_aminoacid(p1BDG, a87, gly).
has_atom(p1BDG, a64, ’CD2’, p(22.4,13.3,65.5)).
has_atom(p1BDG, a64, ’CE2’, p(21.6,14.0,66.4)).
has_atom(p1BDG, a85, ’C’, p(24.6,25.9,57.4)).
has_atom(p1BDG, a85, ’O’, p(24.6,24.8,57.8)).
has_atom(p1BDG, a86, ’N’, p(24.8,27.0,58.3)).
has_atom(p1BDG, a86, ’CA’, p(24.9,26.8,59.7)).

Since 1BDG is a hexose-binding protein, center_coords/2 predicate states the coordinates of the hexose binding center. The has_aminoacid and has_atom predicates state the coordinates of the amino acids and atoms in a neighborhood of 10 Å of the binding site center.

A Santos et al.

A Santos et al. BMC Bioinformatics 2012 13:162   doi:10.1186/1471-2105-13-162

Open Data