The specific applications of the TSR-based method in identifying Zn2+ binding sites of proteases and ACE/ACE2

Abstract

We have developed an alignment-free TSR (Triangular Spatial Relationship)-based computational method for protein structural comparison and motif identification and discovery. To demonstrate the potential applications of the method, we have generated two datasets. One dataset contains five classes: Actin/Hsp70, serine protease (chymotrypsin/trypsin/elastase), ArsC/Prdx2, PKA/PKB/PKC, and AChE/BChE at the hierarchical level 1 and twelve groups at the level 2. The other dataset includes representative proteases and ACE/ACE2. The x,y, z coordinates of the structures were obtained from PDB. We calculated the keys (or features) that represent each structure using the TSR-based method. The dataset and data presented here include additional information that help the readers become aware of specific applications of the TSR-based method in protein clustering, identification and discovery of metal ion binding sites as well as to understand the effect of amino acid grouping on protein 3D structural relationships at both global and local levels.

Keywords

• TSR
• Metal ion binding site
• Protein similarity
• 3D structure
• Alignment-free
• Structural motif