In order to deal correctly with difficulties, modern technology like computer tools and experimental techniques must be used quickly and efficiently. Ligand-binding sites are frequently the beginning point for protein annotation and drug design structures. In recent decades, several computer approaches have been developed for the prediction of binding sites. Knowledge of the 3D structures of protein has been known for long, but new advancements have altered the possibilities drastically in genome sequencing, robotics and bioinformatics. These high-performance structural determination methods can offer strong screening approaches in recent days.