An　efficient　＇soft　docking＇　algorithm　is　described　to　assist　the　prediction　of　protein-protein　association　using　three-dimensional　structures　of　molecules.　The　basic　tools　are　the　＇simplified　protein＇　model　and　the　docking　algorithm　of　Wodak　and　Janin.　The　side　chain　flexibility　of　Arg,　Lys,　Asp,　Glu　and　Met　residues　at　the　protein　surface　is　taken　into　account.　The　complex　type-dependent　filtering　technique　on　the　basis　of　the　geometric　matching,　hydrophobicity　and　electrostatic　complementarity　is　used　to　select　candidate　binding　modes.　Subsequently,　we　calculate　a　scoring　function　which　includes　electrostatic　and　desolvation　energy　terms.　In　the　44　complexes　tested　including　enzyme-inhibitor,　antibody-antigen　and　other　complexes,　native-like　structures　were　all　found,　of　which　30　were　ranked　in　the　top　20.　Thus,　our　soft　docking　algorithm　has　the　potential　to　predict　protein-protein　recognition.