suite was used to superimpose the two linkers placed in the ligand with their counterparts in the protein structure, allowing the creation of the covalent bond between the two molecules prior to docking. An example of such an aligned structure is presented in Figure . Following the alignment procedure, ADT was used to calculate Gasteiger charges 80 and to generate PDBQT files of the rigid and flexible parts of the complex. During the docking, AD treats the protein and the backbone of its reactive site as rigid, and fixes the C α and C β atoms. The ligand is considered as a fully flexible extension of the protein reactive site.