CaviDB: a database of cavities and their features in the structural and conformational space of proteins

Autores
Velez Rueda, Ana Julia; Bulgarelli, Franco Leonardo; Palopoli, Nicolás; Parisi, Gustavo Daniel
Año de publicación
2023
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Proteins are the structural, functional and evolutionary units of cells. On their surface, proteins are shaped into numerous depressions and protrusions that provide unique microenvironments for ligand binding and catalysis. The dynamics, size and chemical properties of these cavities are essential for a mechanistic understanding of protein function. Here, we present CaviDB, a novel database of cavities and their features in known protein structures. It integrates the results of commonly used cavity detection software with protein features derived from sequence, structural and functional analyses. Each protein in CaviDB is linked to its corresponding conformers, which also facilitates the study of conformational changes in cavities. Our initial release includes ∼927 773 distinct proteins, as well as the characterization of 36 136 869 cavities, of which 1 147 034 were predicted to be drug targets. The structural focus of CaviDB provides the ability to compare cavities and their properties from different conformational states of the protein. CaviDB not only aims to provide a comprehensive database that can be used for various aspects of drug design and discovery but also contributes to a better understanding of the fundamentals of protein structure-function relationships. With its unique approach, CaviDB represents an indispensable resource for the large community of bioinformaticians in particular and biologists in general.
Fil: Velez Rueda, Ana Julia. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Bulgarelli, Franco Leonardo. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina
Fil: Palopoli, Nicolás. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Parisi, Gustavo Daniel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Materia
PROTEINS
CAVITIES
DRUG DESIGN
DATABASE
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/219739
Acceder
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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling CaviDB: a database of cavities and their features in the structural and conformational space of proteinsVelez Rueda, Ana JuliaBulgarelli, Franco LeonardoPalopoli, NicolásParisi, Gustavo DanielPROTEINSCAVITIESDRUG DESIGNDATABASEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Proteins are the structural, functional and evolutionary units of cells. On their surface, proteins are shaped into numerous depressions and protrusions that provide unique microenvironments for ligand binding and catalysis. The dynamics, size and chemical properties of these cavities are essential for a mechanistic understanding of protein function. Here, we present CaviDB, a novel database of cavities and their features in known protein structures. It integrates the results of commonly used cavity detection software with protein features derived from sequence, structural and functional analyses. Each protein in CaviDB is linked to its corresponding conformers, which also facilitates the study of conformational changes in cavities. Our initial release includes ∼927 773 distinct proteins, as well as the characterization of 36 136 869 cavities, of which 1 147 034 were predicted to be drug targets. The structural focus of CaviDB provides the ability to compare cavities and their properties from different conformational states of the protein. CaviDB not only aims to provide a comprehensive database that can be used for various aspects of drug design and discovery but also contributes to a better understanding of the fundamentals of protein structure-function relationships. With its unique approach, CaviDB represents an indispensable resource for the large community of bioinformaticians in particular and biologists in general.Fil: Velez Rueda, Ana Julia. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Bulgarelli, Franco Leonardo. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Palopoli, Nicolás. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Parisi, Gustavo Daniel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaOxford University Press2023-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/219739Velez Rueda, Ana Julia; Bulgarelli, Franco Leonardo; Palopoli, Nicolás; Parisi, Gustavo Daniel; CaviDB: a database of cavities and their features in the structural and conformational space of proteins; Oxford University Press; Database; 2023; 1-2023; 1-71758-0463CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/database/article/doi/10.1093/database/baad010/7159200info:eu-repo/semantics/altIdentifier/doi/10.1093/database/baad010info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:52:54Zoai:ri.conicet.gov.ar:11336/219739instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:52:55.594CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv CaviDB: a database of cavities and their features in the structural and conformational space of proteins
title CaviDB: a database of cavities and their features in the structural and conformational space of proteins
spellingShingle CaviDB: a database of cavities and their features in the structural and conformational space of proteins
Velez Rueda, Ana Julia
PROTEINS
CAVITIES
DRUG DESIGN
DATABASE
title_short CaviDB: a database of cavities and their features in the structural and conformational space of proteins
title_full CaviDB: a database of cavities and their features in the structural and conformational space of proteins
title_fullStr CaviDB: a database of cavities and their features in the structural and conformational space of proteins
title_full_unstemmed CaviDB: a database of cavities and their features in the structural and conformational space of proteins
title_sort CaviDB: a database of cavities and their features in the structural and conformational space of proteins
dc.creator.none.fl_str_mv Velez Rueda, Ana Julia
Bulgarelli, Franco Leonardo
Palopoli, Nicolás
Parisi, Gustavo Daniel
author Velez Rueda, Ana Julia
author_facet Velez Rueda, Ana Julia
Bulgarelli, Franco Leonardo
Palopoli, Nicolás
Parisi, Gustavo Daniel
author_role author
author2 Bulgarelli, Franco Leonardo
Palopoli, Nicolás
Parisi, Gustavo Daniel
author2_role author
author
author
dc.subject.none.fl_str_mv PROTEINS
CAVITIES
DRUG DESIGN
DATABASE
topic PROTEINS
CAVITIES
DRUG DESIGN
DATABASE
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Proteins are the structural, functional and evolutionary units of cells. On their surface, proteins are shaped into numerous depressions and protrusions that provide unique microenvironments for ligand binding and catalysis. The dynamics, size and chemical properties of these cavities are essential for a mechanistic understanding of protein function. Here, we present CaviDB, a novel database of cavities and their features in known protein structures. It integrates the results of commonly used cavity detection software with protein features derived from sequence, structural and functional analyses. Each protein in CaviDB is linked to its corresponding conformers, which also facilitates the study of conformational changes in cavities. Our initial release includes ∼927 773 distinct proteins, as well as the characterization of 36 136 869 cavities, of which 1 147 034 were predicted to be drug targets. The structural focus of CaviDB provides the ability to compare cavities and their properties from different conformational states of the protein. CaviDB not only aims to provide a comprehensive database that can be used for various aspects of drug design and discovery but also contributes to a better understanding of the fundamentals of protein structure-function relationships. With its unique approach, CaviDB represents an indispensable resource for the large community of bioinformaticians in particular and biologists in general.
Fil: Velez Rueda, Ana Julia. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Bulgarelli, Franco Leonardo. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina
Fil: Palopoli, Nicolás. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Parisi, Gustavo Daniel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Proteins are the structural, functional and evolutionary units of cells. On their surface, proteins are shaped into numerous depressions and protrusions that provide unique microenvironments for ligand binding and catalysis. The dynamics, size and chemical properties of these cavities are essential for a mechanistic understanding of protein function. Here, we present CaviDB, a novel database of cavities and their features in known protein structures. It integrates the results of commonly used cavity detection software with protein features derived from sequence, structural and functional analyses. Each protein in CaviDB is linked to its corresponding conformers, which also facilitates the study of conformational changes in cavities. Our initial release includes ∼927 773 distinct proteins, as well as the characterization of 36 136 869 cavities, of which 1 147 034 were predicted to be drug targets. The structural focus of CaviDB provides the ability to compare cavities and their properties from different conformational states of the protein. CaviDB not only aims to provide a comprehensive database that can be used for various aspects of drug design and discovery but also contributes to a better understanding of the fundamentals of protein structure-function relationships. With its unique approach, CaviDB represents an indispensable resource for the large community of bioinformaticians in particular and biologists in general.
publishDate 2023
dc.date.none.fl_str_mv 2023-01
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
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://hdl.handle.net/11336/219739
Velez Rueda, Ana Julia; Bulgarelli, Franco Leonardo; Palopoli, Nicolás; Parisi, Gustavo Daniel; CaviDB: a database of cavities and their features in the structural and conformational space of proteins; Oxford University Press; Database; 2023; 1-2023; 1-7
1758-0463
CONICET Digital
CONICET
url http://hdl.handle.net/11336/219739
identifier_str_mv Velez Rueda, Ana Julia; Bulgarelli, Franco Leonardo; Palopoli, Nicolás; Parisi, Gustavo Daniel; CaviDB: a database of cavities and their features in the structural and conformational space of proteins; Oxford University Press; Database; 2023; 1-2023; 1-7
1758-0463
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/database/article/doi/10.1093/database/baad010/7159200
info:eu-repo/semantics/altIdentifier/doi/10.1093/database/baad010
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.13397

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