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dc.contributor.author
Velez Rueda, Ana Julia
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dc.contributor.author
Bulgarelli, Franco Leonardo
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dc.contributor.author
Palopoli, Nicolás
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dc.contributor.author
Parisi, Gustavo Daniel
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dc.date.available
2023-12-11T12:42:54Z
dc.date.issued
2023-01
dc.identifier.citation
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
dc.identifier.issn
1758-0463
dc.identifier.uri
http://hdl.handle.net/11336/219739
dc.description.abstract
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.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Oxford University Press
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dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
PROTEINS
dc.subject
CAVITIES
dc.subject
DRUG DESIGN
dc.subject
DATABASE
dc.subject.classification
Bioquímica y Biología Molecular
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dc.subject.classification
Ciencias Biológicas
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dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
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dc.title
CaviDB: a database of cavities and their features in the structural and conformational space of proteins
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2023-12-07T17:49:29Z
dc.journal.volume
2023
dc.journal.pagination
1-7
dc.journal.pais
Reino Unido
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dc.description.fil
Fil: Velez Rueda, Ana Julia. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
dc.description.fil
Fil: Bulgarelli, Franco Leonardo. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina
dc.description.fil
Fil: Palopoli, Nicolás. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
dc.description.fil
Fil: Parisi, Gustavo Daniel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
dc.journal.title
Database
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/database/article/doi/10.1093/database/baad010/7159200
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1093/database/baad010
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