Abstract
In the former work, we proposed a novel 3D protein structural homology search algorithm based on the Triangle ID comparison method. In that work, we focused a triangle structure consisting of three amino acids and called it as Triangle ID. We assumed that proteins can be characterized by using these Triangle IDs. To prove the validness of this assumption, we developed the homology search tool, did several experiment based on the sample data sets, and showed the validness of our assumption and the scalability of our method. On the other hand, identification of 3D characteristics of protein is required, and we assumed that our Triangle ID method can be used for this purpose. In this study, we propose 3D protein structure clustering by using 3D motifs based on the Triangle ID. The 3D motifs were extracted from the common Triangle IDs which have the same feature and belong to the same protein families. We defined the selectivity criteria, did several experiments, and showed the effectiveness of our proposed approach. We selected protease families as our experiment target, because they are attracted the attention as drug target proteins. Our method opens the possibility of the efficient protein function analysis by 3D motifs based on the Triangle ID.
