TMalphaDB and TMbetaDB

Membrane proteins represent over 25 % of human protein genes and account for more than 60 % of drug targets due to their accessibility from the extracellular environment. The increasing number of available crystal structures of these proteins in the Protein Data Bank permits an initial estimation of...

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Autores: Perea, Marc, Lugtenburg, Ivar, Mayol, Eduardo|||0000-0003-3120-8667, Cordomí Montoya, Arnau|||0000-0002-3848-2928, Deupi, Xavier|||0000-0003-4572-9316, Pardo Carrasco, Leonardo|||0000-0003-1778-7420, Olivella, Mireia|||0000-0002-6035-3399
Tipo de recurso: artículo
Fecha de publicación:2015
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:254427
Acceso en línea:https://ddd.uab.cat/record/254427
https://dx.doi.org/urn:doi:10.1186/s12859-015-0699-5
Access Level:acceso abierto
Palabra clave:Membrane proteins
Transmembrane segments
Sequence motifs
Structural distortion
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spelling TMalphaDB and TMbetaDBweb servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteinsPerea, MarcLugtenburg, IvarMayol, Eduardo|||0000-0003-3120-8667Cordomí Montoya, Arnau|||0000-0002-3848-2928Deupi, Xavier|||0000-0003-4572-9316Pardo Carrasco, Leonardo|||0000-0003-1778-7420Olivella, Mireia|||0000-0002-6035-3399Membrane proteinsTransmembrane segmentsSequence motifsStructural distortionMembrane proteins represent over 25 % of human protein genes and account for more than 60 % of drug targets due to their accessibility from the extracellular environment. The increasing number of available crystal structures of these proteins in the Protein Data Bank permits an initial estimation of their structural properties. We have developed two web servers-TMalphaDB for α-helix bundles and TMbetaDB for β-barrels-to analyse the growing repertoire of available crystal structures of membrane proteins. TMalphaDB and TMbetaDB permit to search for these specific sequence motifs in a non-redundant structure database of transmembrane segments and quantify structural parameters such as ϕ and ψ backbone dihedral angles, χ side chain torsion angle, unit bend and unit twist. The structural information offered by TMalphaDB and TMbetaDB permits to quantify structural distortions induced by specific sequence motifs, and to elucidate their role in the 3D structure. This specific structural information has direct implications in homology modeling of the growing sequences of membrane proteins lacking experimental structure. TMalphaDB and TMbetaDB are freely available at http://lmc.uab.cat/TMalphaDB and http://lmc.uab.cat/TMbetaDB. 22015-01-0120152015-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/254427https://dx.doi.org/urn:doi:10.1186/s12859-015-0699-5reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengMinisterio de Economía y Competitividad https://doi.org/10.13039/501100003329 SAF2013-48271-C2-2-RMinisterio de Ciencia e Innovación https://doi.org/10.13039/501100004837 CD09/00150open 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:2544272026-06-06T12:50:31Z
dc.title.none.fl_str_mv TMalphaDB and TMbetaDB
web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins
title TMalphaDB and TMbetaDB
spellingShingle TMalphaDB and TMbetaDB
Perea, Marc
Membrane proteins
Transmembrane segments
Sequence motifs
Structural distortion
title_short TMalphaDB and TMbetaDB
title_full TMalphaDB and TMbetaDB
title_fullStr TMalphaDB and TMbetaDB
title_full_unstemmed TMalphaDB and TMbetaDB
title_sort TMalphaDB and TMbetaDB
dc.creator.none.fl_str_mv Perea, Marc
Lugtenburg, Ivar
Mayol, Eduardo|||0000-0003-3120-8667
Cordomí Montoya, Arnau|||0000-0002-3848-2928
Deupi, Xavier|||0000-0003-4572-9316
Pardo Carrasco, Leonardo|||0000-0003-1778-7420
Olivella, Mireia|||0000-0002-6035-3399
author Perea, Marc
author_facet Perea, Marc
Lugtenburg, Ivar
Mayol, Eduardo|||0000-0003-3120-8667
Cordomí Montoya, Arnau|||0000-0002-3848-2928
Deupi, Xavier|||0000-0003-4572-9316
Pardo Carrasco, Leonardo|||0000-0003-1778-7420
Olivella, Mireia|||0000-0002-6035-3399
author_role author
author2 Lugtenburg, Ivar
Mayol, Eduardo|||0000-0003-3120-8667
Cordomí Montoya, Arnau|||0000-0002-3848-2928
Deupi, Xavier|||0000-0003-4572-9316
Pardo Carrasco, Leonardo|||0000-0003-1778-7420
Olivella, Mireia|||0000-0002-6035-3399
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Membrane proteins
Transmembrane segments
Sequence motifs
Structural distortion
topic Membrane proteins
Transmembrane segments
Sequence motifs
Structural distortion
description Membrane proteins represent over 25 % of human protein genes and account for more than 60 % of drug targets due to their accessibility from the extracellular environment. The increasing number of available crystal structures of these proteins in the Protein Data Bank permits an initial estimation of their structural properties. We have developed two web servers-TMalphaDB for α-helix bundles and TMbetaDB for β-barrels-to analyse the growing repertoire of available crystal structures of membrane proteins. TMalphaDB and TMbetaDB permit to search for these specific sequence motifs in a non-redundant structure database of transmembrane segments and quantify structural parameters such as ϕ and ψ backbone dihedral angles, χ side chain torsion angle, unit bend and unit twist. The structural information offered by TMalphaDB and TMbetaDB permits to quantify structural distortions induced by specific sequence motifs, and to elucidate their role in the 3D structure. This specific structural information has direct implications in homology modeling of the growing sequences of membrane proteins lacking experimental structure. TMalphaDB and TMbetaDB are freely available at http://lmc.uab.cat/TMalphaDB and http://lmc.uab.cat/TMbetaDB.
publishDate 2015
dc.date.none.fl_str_mv 2
2015-01-01
2015
2015-01-01
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/254427
https://dx.doi.org/urn:doi:10.1186/s12859-015-0699-5
url https://ddd.uab.cat/record/254427
https://dx.doi.org/urn:doi:10.1186/s12859-015-0699-5
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 SAF2013-48271-C2-2-R
Ministerio de Ciencia e Innovación https://doi.org/10.13039/501100004837 CD09/00150
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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score 15,300719

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