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This similarity value has nothing to do with the FTrees similarity. It is very similar to the RMSD value given in the previous column. The RMS value however, is strictly restricted to calculate the RMSD between the 2 coordinates assigned to one atom: the docking solution coordinates and the reference coordinates. The similarity value is more flexible. This calculates an RMS between the docking coordinates of an atom and the reference coordinates of the nearest atom of the same SYBYL atom type. For example, a large molecule docked back to front will have a bad (high) RMSD but could possibly still achieve a good (low) similarity index.