To validate our docking procedure, we have plotted the best RMSD for all protein-ligand complexes as well as the RMSD for the best-scored pose as the cumulative frequency for all 'Top Percent' values and varying degrees of protein flexibility in the left-hand panels of Figure . These plots indicate that the use of larger 'Top Percent' values such as 20%, 50%, and 100% produce more poses within 2.0 Å than lower 'Top Percent' values (0.5% -10%). For the semi-flexible (Figure )method, the 'Top Percent' value of 20% yielded the greatest number of poses within 2.0 Å of the crystal pose. The success rate, ability to produce at least one "good" pose, at this value is 91%. If one considers all 'Top Percent' values investigated, the overall success rate of the semi-flexible method is 94%. Excluding the three peptides present in PDBbind (which are generally ignored in docking studies), there are only 12 co-crystals where CANDOCK fails to find a single "good" pose.