I have an article in which two types of multiple protein structures docking  are described (multiple docking and ensemble docking) but it is not clearly stated how these approaches differ.
Ensemble docking refers to the approach of generating multiple structures of the target molecule using molecular dynamics simulation and study docking to this ensemble of target structures. Multiple docking refers to the breaking down of the target structure into smaller components that are then used for docking in various combinations. Both of these approaches try to account for conformational changes of the target protein.