The software that generates AANT uses HBPLUS to predict hydrogen bond interactions between single bases and single amino acid residues within these complexes. The AANT software uses this information to break down a single PDB structure into scores of individual interactions between either the base, sugar, or phosphate of a nucleotide and the side chain or peptide backbone of a amino acid. The software then superimposes all the interactions between a particular moiety of a nucleotide and a particular moiety of a amino acid residue into a single 3D model, centering on a particular point in the base, sugar, or phosphate. The AANT software then groups geometrically similar interactions into clusters. Refer to the paper for details.
You can visualize the AANT models using the simple web interface, which relies on the Chime plug-in. You can also download these models for further analysis using publicly available tools for manipulating PDB structures.