Abstract: A novel docking algorithm based on the geometric match is proposed for protein-phage peptide complexes. The radii of gyration of protein-phage peptide complexes are used as the criterion of geometric match on the interface, which can be used to screen out the ligand structures with a good geometry fit without any prior description for the contact surface. The energy is evaluated for the structures with a good geometry fit. The algorithm is used to calculate the rigid and flexible docking of four protein phage peptide complexes and predict successfully the native like structures of phage peptides.

Key words: Docking calculation, Geometric fit on surface, Protein-phage peptide complexes