Aggrescan3D (A3D) 2.0

Protein aggregation is a hallmark of a growing number of human disorders and constitutes a major bottleneck in the manufacturing of therapeutic proteins. Therefore, there is a strong need of in-silico methods that can anticipate the aggregative properties of protein variants linked to disease and as...

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Autores: Kuriata, Aleksander, Iglesias, Valentin|||0000-0002-6133-0869, Pujols Pujol, Jordi|||0000-0001-9424-5866, Kurcinski, Mateusz, Kmiecik, Sebastian|||0000-0001-7623-0935, Ventura, Salvador|||0000-0002-9652-6351
Tipo de recurso: artículo
Fecha de publicación:2019
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:222827
Acceso en línea:https://ddd.uab.cat/record/222827
https://dx.doi.org/urn:doi:10.1093/nar/gkz321
Access Level:acceso abierto
Palabra clave:Algorithms
Humans
Information dissemination
Internet
Protein aggregates
Protein aggregation, pathological
Protein multimerization
Protein stability
Proteins
Software
Solubility
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spelling Aggrescan3D (A3D) 2.0prediction and engineering of protein solubilityKuriata, AleksanderIglesias, Valentin|||0000-0002-6133-0869Pujols Pujol, Jordi|||0000-0001-9424-5866Kurcinski, MateuszKmiecik, Sebastian|||0000-0001-7623-0935Ventura, Salvador|||0000-0002-9652-6351AlgorithmsHumansInformation disseminationInternetProtein aggregatesProtein aggregation, pathologicalProtein multimerizationProtein stabilityProteinsSoftwareSolubilityProtein aggregation is a hallmark of a growing number of human disorders and constitutes a major bottleneck in the manufacturing of therapeutic proteins. Therefore, there is a strong need of in-silico methods that can anticipate the aggregative properties of protein variants linked to disease and assist the engineering of soluble protein-based drugs. A few years ago, we developed a method for structure-based prediction of aggregation properties that takes into account the dynamic fluctuations of proteins. The method has been made available as the Aggrescan3D (A3D) web server and applied in numerous studies of protein structure-aggregation relationship. Here, we present a major update of the A3D web server to version 2.0. The new features include: extension of dynamic calculations to significantly larger and multimeric proteins, simultaneous prediction of changes in protein solubility and stability upon mutation, rapid screening for functional protein variants with improved solubility, a REST-ful service to incorporate A3D calculations in automatic pipelines, and a new, enhanced web server interface. A3D 2.0 is freely available at: http://biocomp.chem.uw.edu.pl/A3D2/. 22019-01-0120192019-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/222827https://dx.doi.org/urn:doi:10.1093/nar/gkz321reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengAgencia Estatal de Investigación https://doi.org/10.13039/501100011033 BIO2016-78310-Ropen 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, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by-nc/3.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2228272026-06-06T12:50:31Z
dc.title.none.fl_str_mv Aggrescan3D (A3D) 2.0
prediction and engineering of protein solubility
title Aggrescan3D (A3D) 2.0
spellingShingle Aggrescan3D (A3D) 2.0
Kuriata, Aleksander
Algorithms
Humans
Information dissemination
Internet
Protein aggregates
Protein aggregation, pathological
Protein multimerization
Protein stability
Proteins
Software
Solubility
title_short Aggrescan3D (A3D) 2.0
title_full Aggrescan3D (A3D) 2.0
title_fullStr Aggrescan3D (A3D) 2.0
title_full_unstemmed Aggrescan3D (A3D) 2.0
title_sort Aggrescan3D (A3D) 2.0
dc.creator.none.fl_str_mv Kuriata, Aleksander
Iglesias, Valentin|||0000-0002-6133-0869
Pujols Pujol, Jordi|||0000-0001-9424-5866
Kurcinski, Mateusz
Kmiecik, Sebastian|||0000-0001-7623-0935
Ventura, Salvador|||0000-0002-9652-6351
author Kuriata, Aleksander
author_facet Kuriata, Aleksander
Iglesias, Valentin|||0000-0002-6133-0869
Pujols Pujol, Jordi|||0000-0001-9424-5866
Kurcinski, Mateusz
Kmiecik, Sebastian|||0000-0001-7623-0935
Ventura, Salvador|||0000-0002-9652-6351
author_role author
author2 Iglesias, Valentin|||0000-0002-6133-0869
Pujols Pujol, Jordi|||0000-0001-9424-5866
Kurcinski, Mateusz
Kmiecik, Sebastian|||0000-0001-7623-0935
Ventura, Salvador|||0000-0002-9652-6351
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Algorithms
Humans
Information dissemination
Internet
Protein aggregates
Protein aggregation, pathological
Protein multimerization
Protein stability
Proteins
Software
Solubility
topic Algorithms
Humans
Information dissemination
Internet
Protein aggregates
Protein aggregation, pathological
Protein multimerization
Protein stability
Proteins
Software
Solubility
description Protein aggregation is a hallmark of a growing number of human disorders and constitutes a major bottleneck in the manufacturing of therapeutic proteins. Therefore, there is a strong need of in-silico methods that can anticipate the aggregative properties of protein variants linked to disease and assist the engineering of soluble protein-based drugs. A few years ago, we developed a method for structure-based prediction of aggregation properties that takes into account the dynamic fluctuations of proteins. The method has been made available as the Aggrescan3D (A3D) web server and applied in numerous studies of protein structure-aggregation relationship. Here, we present a major update of the A3D web server to version 2.0. The new features include: extension of dynamic calculations to significantly larger and multimeric proteins, simultaneous prediction of changes in protein solubility and stability upon mutation, rapid screening for functional protein variants with improved solubility, a REST-ful service to incorporate A3D calculations in automatic pipelines, and a new, enhanced web server interface. A3D 2.0 is freely available at: http://biocomp.chem.uw.edu.pl/A3D2/.
publishDate 2019
dc.date.none.fl_str_mv 2
2019-01-01
2019
2019-01-01
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/222827
https://dx.doi.org/urn:doi:10.1093/nar/gkz321
url https://ddd.uab.cat/record/222827
https://dx.doi.org/urn:doi:10.1093/nar/gkz321
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 BIO2016-78310-R
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by-nc/3.0/
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-nc/3.0/
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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