The structures were created by entering the required parameters into the CHARMM-GUI, which subsequently analyzed the data to build precise and detailed 3D models. These models were then utilized for additional research and simulations. The aptamer's fundamental structure (aptamer sequence), which was discovered through earlier research, served as the basis for the structural predictions of the aptamer. This step involves uploading the aptamer base pair sequence to the Vfold2D website to obtain the aptamer's secondary structure . These were useful in figuring out 3D aptamer structure and function. In dot-bracket notation, dots represent non-bonded nucleotides, and a pair of opened and closed parentheses represent bonded base pairs. Vfold3D was used to model the tertiary structure. Several web servers offer the lowest energy structure, or the most stable structure, to validate the structure. HDOCK2.4 simulated aptamer binding to the HER2 receptor . A graph neural network (GNN) was employed to obtain the receptor's binding site, known as GrASP . Additionally, the P2Rank webserver was used for the same objective.