CASP2 MOLECULAR DOCKING PREDICTIONS WITH THE LIGIN SOFTWARE

Seven docking predictions were made with the LIGIN program. Tn six cas es the location of the binding pocket was identified correctly by syst ematically docking everywhere within the protein structure. In two cas es the Ligand was docked to within 1.8 Angstrom RMSD of the experiment ally determined structure, LIGIN has not been optimized to deal with h ighly flexible ligands that dock at the surface of proteins. Consequen tly, in three cases the exposed part of the ligand was docked poorly, although the buried parts were docked well, and made similar atomic co ntacts with the protein as in the experimentally determined structure. (C) 1998 Wiley-Liss, Inc.