Nucleic Acids Research, 2009, Vol. 37, Web Server issue W489 Figure 2. Result page of @TOME-2. Example of results after a background calculation for the yeast protein Ssu72 followed by selection of ligands. Residues of selected experimental templates are colored according to secondary structure (red, blue and green stand for helix, strand and loop, respectively) or according to their distance to the selected ligands (Boxes in yellow, orange or red for distances below 8, 6 and 4 A˚, respectively). Figure 3. Result page for on-the-ﬂy comparative docking. A comparative docking was performed using a set of selected ligands and models deduced from the alignment of ssu72 and the template PDB1D1Q. The two partial models were built using TITO or SCWRL. Ranking of ligand poses are done according to MedusaScore or AutoDOCK (for the TITO model and the SCWRL model, respectively). Close view of the protein–ligand complex between ssu72 (TITO partial model) and 4-nitro-phenyl phosphate is shown in the left panel using the Jmol applet. biochemical analyses (32). The lost of the catalytic resi- dues can be also derived from the sequence–structure com- parison in agreement with the binding of an eﬀector by the repressor without chemical modiﬁcation. Example 3: Rop2. More recently, we used @TOME-2 to conﬁrm the absence of ligand binding in the active site pocket of an atypical protein kinase from Toxoplasma gondii. While ATP transfer could be successfully