Examination of Shape

Here we carry out an examination of shape complementarity as a criterion in protein{protein docking and binding. Speci cally, we examine the quality of shape complementarity as a critical determinant not only in the docking of 26 protein{protein \bound", complexed cases, but in particular, of 19 \unbound" protein{protein cases, where the structures have been determined separately. In all cases, entire molecular surfaces are utilized in the docking, with no consideration of the location of the active site, or of particular residues/atoms in either the receptor or the ligand which participate in the binding. To evaluate the goodness of the strictly geometry-based shape complementarity in the docking process as compared to the main favorable and unfavorable energy components, we study systematically a potential correlation between each of these components and the RMSD of the \unbound" protein{protein cases. Speci cally, we examine the non-polar buried surface area, polar buried surface area, buried surface area relating to groups bearing unsatis ed buried charges, and the number of hydrogen bonds in all docked protein{protein interfaces. For these cases, where the two proteins have been crystallized separately, and where entire molecular surfaces are considered without a prede nition of the binding site, no correlation is observed. None of these parameters appears to consistently improve on shape complementarity in the docking of unbound molecules. These ndings argue that simplicity in the docking process, utilizing geometrical shape criteria may capture many of the essential features in protein{protein docking. In particular, they further re-enforce the long held notion of the importance of molecular surface shape complementarity in the binding, and hence in docking. This is particularly interesting in light of the fact that the structures of the docked pairs have been determined separately, allowing side chains on the surface of the proteins to move relatively freely. This study has been enabled by our e cient, computer-vision based docking algorithms. The fast CPU matching times, on the order of minutes on a PC, allow such large scale docking experiments of large molecules, which may not be feasible by other techniques.