TY - JOUR
T1 - RepeatsDB in 2021
T2 - Improved data and extended classification for protein tandem repeat structures
AU - Paladin, Lisanna
AU - Bevilacqua, Martina
AU - Errigo, Sara
AU - Piovesan, Damiano
AU - Mičetić, Ivan
AU - Necci, Marco
AU - Monzon, Alexander Miguel
AU - Fabre, Maria Laura
AU - Lopez, Jose Luis
AU - Nilsson, Juliet F.
AU - Rios, Javier
AU - Menna, Pablo Lorenzano
AU - Cabrera, Maia
AU - Buitron, Martin Gonzalez
AU - Kulik, Mariane Gonçalves
AU - Fernandez-Alberti, Sebastian
AU - Fornasari, Maria Silvina
AU - Parisi, Gustavo
AU - Lagares, Antonio
AU - Hirsh, Layla
AU - Andrade-Navarro, Miguel A.
AU - Kajava, Andrey V.
AU - Tosatto, Silvio C.E.
N1 - Publisher Copyright:
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
PY - 2021/1/8
Y1 - 2021/1/8
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85099429028&partnerID=8YFLogxK
U2 - 10.1093/nar/gkaa1097
DO - 10.1093/nar/gkaa1097
M3 - Article
C2 - 33237313
AN - SCOPUS:85099429028
SN - 0305-1048
VL - 49
SP - D452-D457
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -