EVALUATION OF THE CASP2 DOCKING SECTION

The docking section of CASP2 is reviewed. Seven small molecule ligand- protein targets and one protein-protein target were available for pred ictions, Many of the small molecule ligand complexes involved serine p roteases. Overall results for the small molecule targets were good, wi th at least one prediction for each target being within 3 Angstrom roo t-mean-square deviation (RMSD) for nearly all targets and within 2 Ang strom RMSD for over half the targets, However no single docking method seemed to consistently perform best, In addition, the predictions clo sest to tile experimental results were not always those ranked the hig hest, pointing out that the evaluation (scoring) of potential solution s is still an area Chef, needs improvement, The protein-protein target proved more difficult, None of the predictions did well in reproducin g the geometry of the complex, although in many cases the interacting surfaces of the two proteins were predicted with reasonable accuracy. This target consisted of two large proteins and, therefore was a deman ding target for docking methods. (C) 1998 Wiley-Liss, Inc.