Protein+Protein+Achievements

The ICM-Pro protein-protein docking methodology was originally successfully applied to the prediction of an antibody-lysozyme complex [Totrov, 1994] and was later tested in a blind prediction contest [Strynadka, 1996]. The ICM-Pro protein-protein docking methods incorporate a two-step procedure incorporating rigid-body docking followed by ICM side-chain optimization [Fernandez-Recio, 2002; Fernandez-Recio, 2002; Fernandez-Recio, 2003]. Using this method and incorporating solvation with a screened charge electrostatic model it has been tested on a benchmark of 24 protein-protein complexes in which the three-dimensional structures of their subunits (bound and free) were available. The rank of the near-native conformation in a list of candidate docking solutions was <20 in 85% of complexes with no major backbone motion on binding. Among them, as many as 7 out of 11 (64%) protease-inhibitor complexes can be successfully predicted as the highest rank conformations.