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

The increasing availability of protein structures presents new opportunities for detecting homologous proteins. While global alignment methods are widely used and generally effective, they often struggle to identify related structures obscured by differences in protein size and domain architecture. To address this limitation, we introduce Structome-TM, a web server for protein structure comparison and phylogenetic analysis using TM-score as a metric. By emphasizing local structural alignments, Structome-TM improves the detection of homologous proteins that global methods might overlook. With a user-friendly interface and efficient pairwise comparisons, Structome-TM expands the structural neighbourhood landscape and facilitates phylogenetic reconstruction.