The Molecular Graphics Laboratory Forum

For me autodock is good software for docking of small molecules.I am co-author of 3 papers in which i have cited autodock and i trust .But one thing always create problem ...that is docking pose selection. I use to validate the docking procedure by redocking the co-crystallized conformation of inhibitor and getting it back after docking procedure. I have found that top ranked poses are not always the same as co -crystallized conformation.If problem exists with already known complexes ,then how we can correctly predict for new class of inhibitors.I need detailed suggestion in this regard
that how to select best pose.