Structural bioinformatics is concerned with computational approaches to predict and analyze the spatial structure of proteins and nucleic acids by using different tools and techniques. The aim of present study was to carry out the homology modeling study of AC1 Rep protein and docking between α-lactalbumin and Rep protein of Begomovirus by using modeling and docking (Hex 6.3) softwares. This model show that 35% identity is enough for receptor based antiviral agent designing. The closest homologue of Rep protein was 1L2M|A, with the highest sequence identity of 81% that was selected as representative model using homology modeling softwares. The model was validated by using protein structure checking tools such as RAMPAGE server and Prochek for reliability. On the basis of RMS and energy values, the best docking orientation -1.00 was selected. This study will be used for the screening of inhibitors against Begomoviral proteins and can be further applied in future antiviral agent designing.