The use of computational methods for constructing a protein model to support experimental findings aid in answering a great number of questions about the mechanisms underlying various scientific processes. Constructing a protein model and molecular docking computationally can present a clear explanation of biological process integrating to experimental findings. One of the most precise methods currently available is detecting a homolog to a specific amino acid sequence to use it as a template for modeling. In this paper, we present synthesis of 13.6 ± 2.2nm silver nanoparticles using extracellular filtrate of Aspergillus oryzae and homology modeling of five targeted extracellular proteins, as well as homology prediction for each protein's active site. In addition, a nanoparticle of silver that docks with all five proteins is evaluated in silico. According to the results, only 32 out of 50 top 10 solutions for each protein contained polar oxygen or nitrogen atom neighbors. Seven of the 50 solutions for FAD-dependent oxidoreductase contained the greatest number of detectable polar neighbors (six measurements). This finding supports the hypothesis that extracellular fungal proteins play a crucial role in capping silver nanoparticles at various positions and preventing aggregation and sedimentation of nanoparticles. Through homology modeling and docking, we reveal the interaction between FAD-dependent oxidoreductase and silver nanoparticles for the first time.