Table 1.

A typical example of a RMSD (in Å) clustering analysis of a 10 “runs” docking simulation with AutoDock 3.0.5

Rank	Sub-Rank	Run	Docked energy	Cluster RMSD	Reference RMSD
1	1	1	-8.99	0.00	4.10
1	2	10	-8.92	0.30	4.12
1	3	4	-8.90	0.37	4.08
1	4	9	-8.90	0.37	4.09
1	5	5	-8.87	0.22	4.15
1	6	8	-8.44	1.00	3.92
2	1	7	-8.27	0.00	5.84
2	2	3	-7.92	0.46	5.71
3	1	6	-7.84	0.00	4.19
4	1	2	-7.80	0.00	5.70

Autodock clusters by first sorting all the docked conformations from lowest (Docked energy, fourth column) to highest energy (in kcal/mol). The best overall docked conformation is used as the ‘seed’ for the first cluster (Rank 1, first column). Then the coordinates of the second best conformation are compared with those of the best to calculate the root-mean square deviation (Cluster RMSD, fifth column) between the two conformations. If the calculated RMSD value is smaller than or equal the specified cut-off, which is 1.0 by default, that conformation is added to the ‘bin’ containing the best conformation. If not, the second becomes the reference for a second ‘bin’ (Rank 2, seventh row). In this example we have four “bins” or clusters. As can be seen from the table, the 10 “runs” generated four clusters. Cluster 1 contains six out of 10 “runs” and so forth. The last column shows the RMSD of the corresponding conformation with respect to a reference ligand position. The bold value is the best estimated docked energy corresponding to the best docked pose expected from experiments [25].