Abstract—Many researchers have reported about angiopoietin-2 (Ang2), which plays vital aspect of tumor Angiogenesis. Literature studies confirm that aptamers generated by in vitro selection strategy (systematic evolution of ligands by exponential enrichment, SELEX) has the ability to bind and inhibit Ang2 in vitro. A comparative simulation was performed between aptamers and Ang2 in computational environment using Discovery Studio 3.5. ZDOCK which uses Pairwise Shape Complementary as scoring function was performed for simulation, along with ZRANK which assess accurately reranking the rigid body docking results from ZDOCK. From this approach, our computational results showed consistent to in vitro results, thus providing ZDOCK with ZRANK as an alternative method for computational selection of best binding aptamers. This study also presents the binding interface between Ang2/aptamers which can be informative in the future study.