| Autor: |
Malik, Ashar J, Langer, Desiree, Verma, Chandra S, Poole, Anthony M, Allison, Jane R |
| Předmět: |
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| Zdroj: |
Bioinformatics Advances; 2023, Vol. 3 Issue 1, p1-10, 10p |
| Abstrakt: |
Summary Protein structures carry signal of common ancestry and can therefore aid in reconstructing their evolutionary histories. To expedite the structure-informed inference process, a web server, Structome, has been developed that allows users to rapidly identify protein structures similar to a query protein and to assemble datasets useful for structure-based phylogenetics. Structome was created by clustering ∼ 94 % of the structures in RCSB PDB using 90% sequence identity and representing each cluster by a centroid structure. Structure similarity between centroid proteins was calculated, and annotations from PDB, SCOP, and CATH were integrated. To illustrate utility, an H3 histone was used as a query, and results show that the protein structures returned by Structome span both sequence and structural diversity of the histone fold. Additionally, the pre-computed nexus-formatted distance matrix, provided by Structome, enables analysis of evolutionary relationships between proteins not identifiable using searches based on sequence similarity alone. Our results demonstrate that, beginning with a single structure, Structome can be used to rapidly generate a dataset of structural neighbours and allows deep evolutionary history of proteins to be studied. Availability and Implementation Structome is available at: https://structome.bii.a-star.edu.sg. [ABSTRACT FROM AUTHOR] |
| Databáze: |
Complementary Index |
| Externí odkaz: |
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