Here, we propose a rigorous scoring scheme called DockScore which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed.  DockScore was first trained on a set of 30 protein-protein complexes to determine the weights for different parameters.  We tested the ability of DockScore to discriminate likely dimer interactions that differ substantially within a homologous family and also demonstrate that DOCKSCORE can distinguish correct pose for all 10 recent CAPRI targets.
DockScore
Molecular interactions can also be studied computationally using the approach named as Molecular Docking.  Molecular docking employs search algorithms to predict the possible conformations for interacting partners and then calculates interaction energies. 
Molecular Docking