Comparative Analysis of Structural Alignment Algorithms for Protein-Protein Interfaces in Template-Based Docking Studies

Protein-protein interactions are pivotal for various functions within living organisms. Understanding their underlying mechanisms holds significant potential for unraveling cellular processes. There are several methods to identify protein-protein interactions, including but not limited to template-based docking. The power of template docking lies in the template library selection and the quality of structural alignment. Within the scope of our investigation, we specifically delve into the performance of four structural alignment algorithms on one protein interface and four protein structure benchmark sets. This study places particular emphasis on assessing these tools on protein interfaces, composed of non-continuous structure segments, as these interfaces play a crucial role in protein interactions, especially in the context of template-based docking. Notably, our findings indicate that TM-align, despite not being explicitly designed for sequence-order independent alignment, exhibits comparable performance to tools tailored for this purpose while executing in a considerably shorter time frame. Therefore, TM-align emerges as a promising candidate for the crucial structural alignment step in template-docking pipelines.