A genetic algorithm (GA) for protein-protein docking is described, in which
the proteins are represented by dot surfaces calculated using the Connolly
program. The GA is used to move the surface of one protein relative to the
other to locate the area of greatest surface complementarity between the t
wo. Surface dots are deemed complementary if their normals are opposed, the
ir Connolly shape type is complementary, and their hydrogen bonding or hydr
ophobic potential is fulfilled. Overlap of the protein interiors is penaliz
ed. The GA is tested on 34 large protein-protein complexes where one or bot
h proteins has been crystallized separately. Parameters are established for
which 30 of the complexes have at least one near-native solution ranked in
the top 100, We have also successfully reassembled a 1,400-residue heptame
r based on the top-ranking GA solution obtained when docking two bound subu
nits, Proteins 2001;44:44-56. (C) 2001 Wiley-Liss, Inc.