Background: Porphyromonas gingivalis is one of the etiological agents in the initiation of combined periodontal-endodontic (perio-endo) lesions. Successful treatment of perio-endo lesions with photo activated disinfection (PAD) as a novel therapeutic approach depends on the selection of an appropriate target site, specific photosensitizer (PS), and wavelength of light. Since the fimbrillin (FimA) is the most important pathogenic agent in P. gingivalis it was evaluated as a target site against PAD with toluidine blue 0 (TBO) as a PS. Materials and methods: We evaluated the potential of FimA using a number of bioinformatic tools and computer simulation molecular modeling. In silico analysis was done to predict the hierarchical nature of structure, topology, backbone, physicochemical properties, and functional characterization of FimA. Results: The predicted structure of FimA exhibited that it is an anionic protein with negative charge (-7.00) in pH7 and random coil which dominates other secondary structures located outside the cell. It has three motifs with seven ligand binding site residues and one active site residue which can be a site of interaction for cationic TBO. Conclusion: Based on the results of this study cationic TBO tends to interact with FimA during PAD as a major target to increase the efficiency of treatment of perio-endo lesions. (C) 2016 Elsevier B.V. All rights reserved.