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. 2021 Jan 8;49(D1):D452-D457.
doi: 10.1093/nar/gkaa1097.

RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures

Lisanna Paladin  1 , Martina Bevilacqua  1 , Sara Errigo  1 , Damiano Piovesan  1 , Ivan Mičetić  1 , Marco Necci  1 , Alexander Miguel Monzon  1 , Maria Laura Fabre  2 , Jose Luis Lopez  2 , Juliet F Nilsson  2 , Javier Rios  3 , Pablo Lorenzano Menna  3 , Maia Cabrera  3 , Martin Gonzalez Buitron  3 , Mariane Gonçalves Kulik  4 , Sebastian Fernandez-Alberti  3 , Maria Silvina Fornasari  3 , Gustavo Parisi  3 , Antonio Lagares  2 , Layla Hirsh  5 , Miguel A Andrade-Navarro  4 , Andrey V Kajava  6 , Silvio C E Tosatto  1
Affiliations

RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures

Lisanna Paladin et al. Nucleic Acids Res. .

Abstract

The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein tandem repeats are ubiquitous in all branches of the tree of life. The accumulation of solved repeat structures provides new possibilities for classification and detection, but also increasing the need for annotation. Here we present RepeatsDB 3.0, which addresses these challenges and presents an extended classification scheme. The major conceptual change compared to the previous version is the hierarchical classification combining top levels based solely on structural similarity (Class > Topology > Fold) with two new levels (Clan > Family) requiring sequence similarity and describing repeat motifs in collaboration with Pfam. Data growth has been addressed with improved mechanisms for browsing the classification hierarchy. A new UniProt-centric view unifies the increasingly frequent annotation of structures from identical or similar sequences. This update of RepeatsDB aligns with our commitment to develop a resource that extracts, organizes and distributes specialized information on tandem repeat protein structures.

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Figures

Figure 1.
Figure 1.
RepeatsDB classification. The new levels of RepeatsDB classification will discriminate finer structural and functional differences. RepeatsDB topology 4.4 includes beta-propeller regions. The folds in topology 4.4 are distinguished by the number of units (in propellers called ‘blades’), while the clans by the specific secondary structure content and the relative orientation of the blades, as well as the overall shape of the region.
Figure 2.
Figure 2.
(A) RepeatsDB Browse page. This features the classification tree (top) and details of the classification level selected in the tree (bottom). It includes a summary table of the level statistics, image of a representative structure, histogram of unit numbers over per region and a table including all entries belonging to the selected level. (B) UniProt entry page. This shows details of the entry and the consensus repeat annotation (top), Feature Viewer with repeat data for all PDB chains mapped to the UniProt entry (center), PDB section showing repeat data on the sequence and structure of the selected PDB (bottom).
See this image and copyright information in PMC

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