Prediction of multiple binding modes is one of the greatest challenges in
protein-protein docking. As illustrated here, three VHH domains bind to the
pancreatic 
-amylase with distinct binding modes,
including in the major pocket (1KXQ), in a minor groove (1KXT) and on a flat
surface (1KXV). A docking test was conducted on each of the three complexes.
Among the 100 docked complexes, the native and near-native complexes were
correctly identified and the lowest r.m.s.d. from the native complex was 1.57
Å for 1KXQ. For further details, see Lei and Duan, pages 837-845.
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