CAPS-DB: A structural classification of helix-capping motifs

The regions of the polypeptide chain immediately preceding or following an α-helix are known as Nt- and Ct cappings, respectively. Cappings play a central role stabilizing α-helices due to lack of intrahelical hydrogen bonds in the first and last turn. Sequence patterns of amino acid type preference...

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Detalles Bibliográficos
Autores: Segura, Joan, Oliva Miguel, Baldomero, Fernández Fuentes, Narcís
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2012
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/23345
Acceso en línea:http://hdl.handle.net/10230/23345
http://dx.doi.org/10.1093/nar/gkr879
Access Level:acceso abierto
Palabra clave:Aminoàcids
Pèptids
Proteïnes -- Estructura
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spelling CAPS-DB: A structural classification of helix-capping motifsSegura, JoanOliva Miguel, BaldomeroFernández Fuentes, NarcísAminoàcidsPèptidsProteïnes -- EstructuraThe regions of the polypeptide chain immediately preceding or following an α-helix are known as Nt- and Ct cappings, respectively. Cappings play a central role stabilizing α-helices due to lack of intrahelical hydrogen bonds in the first and last turn. Sequence patterns of amino acid type preferences have been derived for cappings but the structural motifs associated to them are still unclassified. CAPS-DB is a database of clusters of structural patterns of different capping types. The clustering algorithm is based in the geometry and the (ϕ–ψ)-space conformation of these regions. CAPS-DB is a relational database that allows the user to search, browse, inspect and retrieve structural data associated to cappings. The contents of CAPS-DB might be of interest to a wide range of scientist covering different areas such as protein design and engineering, structural biology and bioinformatics. The database is accessible at: http://www.bioinsilico.org/CAPSDB.Research Councils United Kingdom Academic Fellow scheme (to N.F.F.); internal scholarship awarded by the Leeds Institute of Molecular Medicine (to J.S.M.); MICINN and FEDER (BIO2011-22568) to B.O. Funding for open access charge: Research Councils United Kingdom (RCUK)Oxford University Press201520152012info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/23345http://dx.doi.org/10.1093/nar/gkr879reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésNucleic Acids Research. 2012;40(D1):D479-D485info:eu-repo/grantAgreement/ES/3PN/BIO2011-22568© Segura J, Oliva B, Fernandez-Fuentes N [2012]. Published by Oxford University Press. This is an Open Access article distributed under the terms of a Creative Commons Attribution Licensehttp://creativecommons.org/licenses/by-nc/3.0info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/233452026-06-12T07:21:37Z
dc.title.none.fl_str_mv CAPS-DB: A structural classification of helix-capping motifs
title CAPS-DB: A structural classification of helix-capping motifs
spellingShingle CAPS-DB: A structural classification of helix-capping motifs
Segura, Joan
Aminoàcids
Pèptids
Proteïnes -- Estructura
title_short CAPS-DB: A structural classification of helix-capping motifs
title_full CAPS-DB: A structural classification of helix-capping motifs
title_fullStr CAPS-DB: A structural classification of helix-capping motifs
title_full_unstemmed CAPS-DB: A structural classification of helix-capping motifs
title_sort CAPS-DB: A structural classification of helix-capping motifs
dc.creator.none.fl_str_mv Segura, Joan
Oliva Miguel, Baldomero
Fernández Fuentes, Narcís
author Segura, Joan
author_facet Segura, Joan
Oliva Miguel, Baldomero
Fernández Fuentes, Narcís
author_role author
author2 Oliva Miguel, Baldomero
Fernández Fuentes, Narcís
author2_role author
author
dc.subject.none.fl_str_mv Aminoàcids
Pèptids
Proteïnes -- Estructura
topic Aminoàcids
Pèptids
Proteïnes -- Estructura
description The regions of the polypeptide chain immediately preceding or following an α-helix are known as Nt- and Ct cappings, respectively. Cappings play a central role stabilizing α-helices due to lack of intrahelical hydrogen bonds in the first and last turn. Sequence patterns of amino acid type preferences have been derived for cappings but the structural motifs associated to them are still unclassified. CAPS-DB is a database of clusters of structural patterns of different capping types. The clustering algorithm is based in the geometry and the (ϕ–ψ)-space conformation of these regions. CAPS-DB is a relational database that allows the user to search, browse, inspect and retrieve structural data associated to cappings. The contents of CAPS-DB might be of interest to a wide range of scientist covering different areas such as protein design and engineering, structural biology and bioinformatics. The database is accessible at: http://www.bioinsilico.org/CAPSDB.
publishDate 2012
dc.date.none.fl_str_mv 2012
2015
2015
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/23345
http://dx.doi.org/10.1093/nar/gkr879
url http://hdl.handle.net/10230/23345
http://dx.doi.org/10.1093/nar/gkr879
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Nucleic Acids Research. 2012;40(D1):D479-D485
info:eu-repo/grantAgreement/ES/3PN/BIO2011-22568
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by-nc/3.0
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc/3.0
eu_rights_str_mv openAccess
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:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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