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

PALADIN, LISANNA; BEVILACQUA, MARTINA; ERRIGO, SARA; PIOVESAN, DAMIANO; MI?ETI?, IVAN; NECCI, MARCO; MONZON, ALEXANDER MIGUEL; FABRE, MARIA LAURA; LOPEZ, JOSE LUIS; NILSSON, JULIET F; RIOS, JAVIER; MENNA, PABLO LORENZANO; CABRERA, MAIA; BUITRON, MARTIN GONZALEZ; KULIK, MARIANE GONÇALVES; FERNANDEZ-ALBERTI, SEBASTIAN; FORNASARI, MARIA SILVINA; PARISI, GUSTAVO; LAGARES, ANTONIO; HIRSH, LAYLA; ANDRADE-NAVARRO, MIGUEL A; KAJAVA, ANDREY V; TOSATTO, SILVIO C E

NUCLEIC ACIDS RESEARCH

OXFORD UNIV PRESS

Año: 2021

0305-1048

The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein DataBank (PDB). Protein tandem repeats are ubiquitousin 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 presentRepeatsDB 3.0, which addresses these challengesand presents an extended classification scheme. Themajor conceptual change compared to the previousversion is the hierarchical classification combiningtop 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. Datagrowth has been addressed with improved mechanisms for browsing the classification hierarchy. Anew UniProt-centric view unifies the increasingly frequent annotation of structures from identical or similar sequences. This update of RepeatsDB aligns withour commitment to develop a resource that extracts,organizes and distributes specialized information ontandem repeat protein structures.