Structome: a tool for the rapid assembly of datasets for structural phylogenetics
Ashar J. Malik, Desiree Langer, Chandra S. Verma, Anthony M. Poole, and Jane R. AllisonWelcome to Structome-Q
Structome-Q is a web server designed to streamline the assembly and analysis of protein structure datasets, utilizing the Q-score metric as implemented in GESAMT. Structome originally began as an exploration of protein structure comparisons but has since expanded into multiple specialized resources, necessitating a rebranding to clarify their distinct utilities. This resource is specifically named Structome-Q to emphasize the use of the Q-score, both for identifying structural neighbors and constructing neighbor-joining trees. Users can explore structural neighbors interactively and use "1 - Q-score" as a metric to render distance-based phylogenetic trees. The resource provides a new way for exploring deep evolutionary signals using protein structures. Have a look at Readme to get started.
Enter a PDB identifier and chain (e.g., 1hv4_A) to explore its structural neighbors:
If you use Structome-Q in your research, please cite:
Malik AJ, Langer D, Verma CS, Poole AM & Allison JR (2023)
Structome: a tool for the rapid assembly of datasets for structural phylogenetics.
Bioinformatics Advances 3(1):vbad134.
Figure: Here is an example from our recent publication that shows how to go from a single structure to a structural phylogeny. We started with a single query protein from with the PDB ID: 4uuz_A. Using the Structome-Q server, we rapidly generated this Histone-fold structural phylogeny. The tool takes the input protein and finds the cluster of similar proteins to which the input belongs. It then generated a phylogeny of the 50 cluster centroids most structurally similar to centroid 1p3m_A (X.laevis histone H3 - coloured orange), the centroid of the cluster to which the query protein (4uuz_A) belongs. Note that we use centroids because the number of proteins in each cluster is very large. The Histone-fold phylogeny appears in the format automatically produced by Structome-Q, here coloured by BLASTP E-value. Each label contains the PDB ID and chain of each cluster centroid.