Figure 1.

The query recognizes the binding pocket of any residue containing a pyranose moiety in the envelope glycoprotein gp160 from Human immunodeficiency virus 1 in complex with Homo sapiens immunoglobulins (3u7y). One of the recognized patterns is highlighted in the box. (A) First, the query identifies a pyranose moiety (a ring composed of 5 carbons and an oxygen atom). (B) Then, all residues which include this pattern in their structure are identified. (C) Finally, all the residues that are at most 4Å from any of the pyranose containing residues are detected as well. This ensures all the potential coordination partners are recognized properly. The molecules were visualized using PyMOL.