Structome-TM: complementing dataset assembly for structural phylogenetics by addressing size-based biases

Abstract

Motivation: Harnessing the explosion of protein structure data to uncover deep evolutionary relationships requires effective comparison methods. While widely used global alignment techniques are powerful, they can fail to identify homologous structures that differ significantly in size or domain architecture. Results: To address this limitation, we introduce Structome-TM, a web resource for assembling datasets for distance-based phylogenetic reconstruction. Making use of the Template Modelling score to prioritize local structural similarity, Structome-TM excels at identifying these otherwise obscured relationships, allowing users to build a comprehensive structural neighbourhood of proteins ..