Energetic contributions and cluster sizes for each docking run.

See text for details and materials and methods for column header definitions. a1PW4 corresponds to the PDB ID glycerol-3-phosphate transporter from Escherichia coli and 2HYD* to the modeled open conformation of Sav1688 ABC transporter. bSize of top ranking clusters. Clustering was performed with a 7.5 Å cutoff based on pairwise interface ligand RMSDs, the RMSD of the ligand after fitting on the binding site of the receptor. cThis cluster scored second on the top; the first cluster included only 7 structures and the energetics were very similar (see Table). dRMSd is the average Root mean square displacement from the top four ranking model of a cluster from its top ranking member, calculated on the backbone atoms of the protein and all heavy atoms of the ligand.