Aggregating amyloid resources

Protein aggregation is responsible for several degenerative conditions in humans, and it is also a bottleneck in industrial protein production and storage of biotherapeutics. Bioinformatics tools have been developed to predict and redesign protein solubility more efficiently by understanding the und...

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Autores: Iglesias, Valentin|||0000-0002-6133-0869, Chilimoniuk, Jaroslaw|||0000-0001-5467-018X, Pintado-Grima, Carlos|||0000-0002-8544-959X, Bárcenas, Oriol|||0000-0002-8439-4005, Ventura, Salvador|||0000-0002-9652-6351, Burdukiewicz, Michał|||0000-0001-8926-582X
Tipo de recurso: artículo
Fecha de publicación:2024
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:304843
Acceso en línea:https://ddd.uab.cat/record/304843
https://dx.doi.org/urn:doi:10.1016/j.csbj.2024.10.047
Access Level:acceso abierto
Palabra clave:Amyloid
Bioinformatics
Biotherapeutics
Database
Protein aggregation
Protein solubility
Prion
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spelling Aggregating amyloid resourcesA comprehensive review of databases on amyloid-like aggregationIglesias, Valentin|||0000-0002-6133-0869Chilimoniuk, Jaroslaw|||0000-0001-5467-018XPintado-Grima, Carlos|||0000-0002-8544-959XBárcenas, Oriol|||0000-0002-8439-4005Ventura, Salvador|||0000-0002-9652-6351Burdukiewicz, Michał|||0000-0001-8926-582XAmyloidBioinformaticsBiotherapeuticsDatabaseProtein aggregationProtein solubilityPrionProtein aggregation is responsible for several degenerative conditions in humans, and it is also a bottleneck in industrial protein production and storage of biotherapeutics. Bioinformatics tools have been developed to predict and redesign protein solubility more efficiently by understanding the underlying principles behind aggregation. As more experimental data become available, dedicated resources for storing, indexing, classifying and consolidating experimental results have emerged. These resources vary in focus, including aggregation-prone regions, 3D patches or protein stretches capable of forming amyloid fibrils. Some of these resources also consider the experimental conditions that cause protein aggregation and how they affect the process. This review article explores how protein aggregation databases have evolved and surveys state-of-the-art resources. We highlight their applications, complementarity and existing limitations. Moreover, we showcase the existing symbiosis between amyloid-related databases and predictive tools. To increase the usefulness of our review, we supplement it with a comprehensive list of present and past amyloid databases: https://biogenies.info/amyloid-database-list/. 22024-01-0120242024-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/304843https://dx.doi.org/urn:doi:10.1016/j.csbj.2024.10.047reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengAgencia Estatal de Investigación https://doi.org/10.13039/501100011033 PID2022-137963OB-I00Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2021/SGR-00635open accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:3048432026-06-06T12:50:31Z
dc.title.none.fl_str_mv Aggregating amyloid resources
A comprehensive review of databases on amyloid-like aggregation
title Aggregating amyloid resources
spellingShingle Aggregating amyloid resources
Iglesias, Valentin|||0000-0002-6133-0869
Amyloid
Bioinformatics
Biotherapeutics
Database
Protein aggregation
Protein solubility
Prion
title_short Aggregating amyloid resources
title_full Aggregating amyloid resources
title_fullStr Aggregating amyloid resources
title_full_unstemmed Aggregating amyloid resources
title_sort Aggregating amyloid resources
dc.creator.none.fl_str_mv Iglesias, Valentin|||0000-0002-6133-0869
Chilimoniuk, Jaroslaw|||0000-0001-5467-018X
Pintado-Grima, Carlos|||0000-0002-8544-959X
Bárcenas, Oriol|||0000-0002-8439-4005
Ventura, Salvador|||0000-0002-9652-6351
Burdukiewicz, Michał|||0000-0001-8926-582X
author Iglesias, Valentin|||0000-0002-6133-0869
author_facet Iglesias, Valentin|||0000-0002-6133-0869
Chilimoniuk, Jaroslaw|||0000-0001-5467-018X
Pintado-Grima, Carlos|||0000-0002-8544-959X
Bárcenas, Oriol|||0000-0002-8439-4005
Ventura, Salvador|||0000-0002-9652-6351
Burdukiewicz, Michał|||0000-0001-8926-582X
author_role author
author2 Chilimoniuk, Jaroslaw|||0000-0001-5467-018X
Pintado-Grima, Carlos|||0000-0002-8544-959X
Bárcenas, Oriol|||0000-0002-8439-4005
Ventura, Salvador|||0000-0002-9652-6351
Burdukiewicz, Michał|||0000-0001-8926-582X
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Amyloid
Bioinformatics
Biotherapeutics
Database
Protein aggregation
Protein solubility
Prion
topic Amyloid
Bioinformatics
Biotherapeutics
Database
Protein aggregation
Protein solubility
Prion
description Protein aggregation is responsible for several degenerative conditions in humans, and it is also a bottleneck in industrial protein production and storage of biotherapeutics. Bioinformatics tools have been developed to predict and redesign protein solubility more efficiently by understanding the underlying principles behind aggregation. As more experimental data become available, dedicated resources for storing, indexing, classifying and consolidating experimental results have emerged. These resources vary in focus, including aggregation-prone regions, 3D patches or protein stretches capable of forming amyloid fibrils. Some of these resources also consider the experimental conditions that cause protein aggregation and how they affect the process. This review article explores how protein aggregation databases have evolved and surveys state-of-the-art resources. We highlight their applications, complementarity and existing limitations. Moreover, we showcase the existing symbiosis between amyloid-related databases and predictive tools. To increase the usefulness of our review, we supplement it with a comprehensive list of present and past amyloid databases: https://biogenies.info/amyloid-database-list/.
publishDate 2024
dc.date.none.fl_str_mv 2
2024-01-01
2024
2024-01-01
dc.type.none.fl_str_mv Article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://ddd.uab.cat/record/304843
https://dx.doi.org/urn:doi:10.1016/j.csbj.2024.10.047
url https://ddd.uab.cat/record/304843
https://dx.doi.org/urn:doi:10.1016/j.csbj.2024.10.047
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Agencia Estatal de Investigación https://doi.org/10.13039/501100011033 PID2022-137963OB-I00
Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2021/SGR-00635
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Dipòsit Digital de Documents de la UAB
instname:Universitat Autònoma de Barcelona
instname_str Universitat Autònoma de Barcelona
reponame_str Dipòsit Digital de Documents de la UAB
collection Dipòsit Digital de Documents de la UAB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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