Structome-TM: Complementing Dataset Assembly for Structural Phylogenetics by Addressing Size-Based Biases
Ashar J. Malik, and David B. AscherWelcome to Structome-TM
Structome-TM is a web server designed to enhance the rapid assembly of protein structure datasets and their subsequent analysis by leveraging the TM-score metric as implemented in Foldseek. This approach helps detect meaningful alignments that might be underestimated by methods emphasizing global structural similarity. Structome-TM's user-friendly interface supports efficient exploration of structural neighborhoods, interactive comparison of protein structures, and the construction of neighbor-joining trees using "1 - TM-score" as the distance metric. By complementing Structome-Q (previously Structome published here), Structome-TM provides an alternative methodology for assembling datasets and uncovering deep evolutionary relationships.
Enter a PDB identifier and chain (e.g., 1hv4_A) to explore its structural neighbors:
If you find this resource helpful, please cite these:
Structural Phylogenetics with Confidence , Structome-Q
Figure: Protein structure alignment between hemoglobin from Anser indicus (RCSB PDB accession 1a4f, chain A, 141 amino acids, shown in green) and flavohemoglobin from Saccharomyces cerevisiae (RCSB PDB accession 4g1b, chain A, 399 amino acids, shown in yellow). The Q-score for this alignment is 0.213, whereas the TM-score is 0.803. The lower similarity score from Q-score reflects its global normalization accounting for overall protein sizes. A score of 0.213 indicates that this result will probably be lost in the background noise.