Results of CAPRI T40 predicted by different methods. Top 3000 structures obtained by ASPDock with and without the information of predicted binding sites. Green protein is the double-headed arrowhead protease inhibitor (API-A). Orange residues are the key residues, Leu87 and Lys145. Small balls are mass centres of ligands. There are 3000 ligand-mass centres in each figure, representing top 3000 structures of ligands. The ASP scores are ranked form red to blue color. (A) Native structure of T40. (B) Top 3000 ligands generated by shape complementarity method. (C) Top 3000 ligands generated by ASPDock method. (D) Top 3000 ligands generated by softly restricting ASPDock method.