Studies were undertaken to examine the mechanism of mediation of silver nanoparticles in inhibiting biofilm formation by Pseudomonas aeruginosa through LuxI/LuxR system of signal transduction. This study includes the basic signaling transduction mechanism LasR, QscR, RhlR, and Vfr signaling model systems. The arbitrary homology models built with the I-TASSER server were evaluated and validated with the Qmean web server. Based on the Z-score and the relative square mean distance (RMSD) values, the structures were validated. The interaction results of the nanoparticle with the rigid docking proved the requirement of minimal energy for the inhibition of the protein active site by the silver nanoparticle. This principle docking experiment suggests that the biofilm formation in Gram-negative bacteria can be inhibited by the silver nanoparticles at the signal transduction level.