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

Autores
Paladin, Lisanna; Bevilacqua, Martina; Errigo, Sara; Piovesan, Damiano; Mičetić, Ivan; Necci, Marco; Monzon, Alexander Miguel; Fabre, María Laura; López, José Luis; Nilsson, Juliet Fernanda; Rios, Javier; Lorenzano Menna, Pablo; Cabrera, Maia; González Buitrón, Martín; Gonçalves Kulik, Mariane; Fernández Alberti, Sebastian; Fornasari, Maria Silvina; Parisi, Gustavo Daniel; Lagares, Antonio; Hirsh, Layla; Andrade Navarro, Miguel A.; Kajava, Andrey V.; Tosatto, Silvio C. E.
Año de publicación
2021
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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.
Facultad de Ciencias Exactas
Instituto de Biotecnologia y Biologia Molecular
Materia
Ciencias Exactas
Biología
database
proteins
classification
protein tandem repeat structures
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by/4.0/
Repositorio
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/126608
Acceder
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oai_identifier_str oai:sedici.unlp.edu.ar:10915/126608
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repository_id_str 1329
network_name_str SEDICI (UNLP)
spelling RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structuresPaladin, LisannaBevilacqua, MartinaErrigo, SaraPiovesan, DamianoMičetić, IvanNecci, MarcoMonzon, Alexander MiguelFabre, María LauraLópez, José LuisNilsson, Juliet FernandaRios, JavierLorenzano Menna, PabloCabrera, MaiaGonzález Buitrón, MartínGonçalves Kulik, MarianeFernández Alberti, SebastianFornasari, Maria SilvinaParisi, Gustavo DanielLagares, AntonioHirsh, LaylaAndrade Navarro, Miguel A.Kajava, Andrey V.Tosatto, Silvio C. E.Ciencias ExactasBiologíadatabaseproteinsclassificationprotein tandem repeat structuresThe 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.Facultad de Ciencias ExactasInstituto de Biotecnologia y Biologia Molecular2021-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArticulohttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfD452-D457http://sedici.unlp.edu.ar/handle/10915/126608enginfo:eu-repo/semantics/altIdentifier/issn/1362-4962info:eu-repo/semantics/altIdentifier/issn/0305-1048info:eu-repo/semantics/altIdentifier/pmid/33237313info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkaa1097info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by/4.0/Creative Commons Attribution 4.0 International (CC BY 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-09-03T11:02:23Zoai:sedici.unlp.edu.ar:10915/126608Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-09-03 11:02:23.853SEDICI (UNLP) - Universidad Nacional de La Platafalse
dc.title.none.fl_str_mv RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures
title RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures
spellingShingle RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures
Paladin, Lisanna
Ciencias Exactas
Biología
database
proteins
classification
protein tandem repeat structures
title_short RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures
title_full RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures
title_fullStr RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures
title_full_unstemmed RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures
title_sort RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures
dc.creator.none.fl_str_mv Paladin, Lisanna
Bevilacqua, Martina
Errigo, Sara
Piovesan, Damiano
Mičetić, Ivan
Necci, Marco
Monzon, Alexander Miguel
Fabre, María Laura
López, José Luis
Nilsson, Juliet Fernanda
Rios, Javier
Lorenzano Menna, Pablo
Cabrera, Maia
González Buitrón, Martín
Gonçalves Kulik, Mariane
Fernández Alberti, Sebastian
Fornasari, Maria Silvina
Parisi, Gustavo Daniel
Lagares, Antonio
Hirsh, Layla
Andrade Navarro, Miguel A.
Kajava, Andrey V.
Tosatto, Silvio C. E.
author Paladin, Lisanna
author_facet Paladin, Lisanna
Bevilacqua, Martina
Errigo, Sara
Piovesan, Damiano
Mičetić, Ivan
Necci, Marco
Monzon, Alexander Miguel
Fabre, María Laura
López, José Luis
Nilsson, Juliet Fernanda
Rios, Javier
Lorenzano Menna, Pablo
Cabrera, Maia
González Buitrón, Martín
Gonçalves Kulik, Mariane
Fernández Alberti, Sebastian
Fornasari, Maria Silvina
Parisi, Gustavo Daniel
Lagares, Antonio
Hirsh, Layla
Andrade Navarro, Miguel A.
Kajava, Andrey V.
Tosatto, Silvio C. E.
author_role author
author2 Bevilacqua, Martina
Errigo, Sara
Piovesan, Damiano
Mičetić, Ivan
Necci, Marco
Monzon, Alexander Miguel
Fabre, María Laura
López, José Luis
Nilsson, Juliet Fernanda
Rios, Javier
Lorenzano Menna, Pablo
Cabrera, Maia
González Buitrón, Martín
Gonçalves Kulik, Mariane
Fernández Alberti, Sebastian
Fornasari, Maria Silvina
Parisi, Gustavo Daniel
Lagares, Antonio
Hirsh, Layla
Andrade Navarro, Miguel A.
Kajava, Andrey V.
Tosatto, Silvio C. E.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Ciencias Exactas
Biología
database
proteins
classification
protein tandem repeat structures
topic Ciencias Exactas
Biología
database
proteins
classification
protein tandem repeat structures
dc.description.none.fl_txt_mv 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.
Facultad de Ciencias Exactas
Instituto de Biotecnologia y Biologia Molecular
description 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.
publishDate 2021
dc.date.none.fl_str_mv 2021-01
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Articulo
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://sedici.unlp.edu.ar/handle/10915/126608
url http://sedici.unlp.edu.ar/handle/10915/126608
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/issn/1362-4962
info:eu-repo/semantics/altIdentifier/issn/0305-1048
info:eu-repo/semantics/altIdentifier/pmid/33237313
info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkaa1097
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by/4.0/
Creative Commons Attribution 4.0 International (CC BY 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
Creative Commons Attribution 4.0 International (CC BY 4.0)
dc.format.none.fl_str_mv application/pdf
D452-D457
dc.source.none.fl_str_mv reponame:SEDICI (UNLP)
instname:Universidad Nacional de La Plata
instacron:UNLP
reponame_str SEDICI (UNLP)
collection SEDICI (UNLP)
instname_str Universidad Nacional de La Plata
instacron_str UNLP
institution UNLP
repository.name.fl_str_mv SEDICI (UNLP) - Universidad Nacional de La Plata
repository.mail.fl_str_mv alira@sedici.unlp.edu.ar
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score 13.13397

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