ALIXE: A phase-combination tool for fragment-based molecular replacement

Fragment-based molecular replacement exploits the use of very accurate yet incomplete search models. In the case of the ARCIMBOLDO programs, consistent phase sets produced from the placement and refinement of fragments with Phaser can be combined in order to increase their signal before proceeding t...

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Detalles Bibliográficos
Autores: Millán, Claudia, Jiménez, E., Schuster, A., Diederichs, K., Usón, Isabel
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2020
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/223038
Acceso en línea:http://hdl.handle.net/10261/223038
Access Level:acceso abierto
Palabra clave:Phasing
ARCIMBOLDO
Fragment-based molecular replacement
Combination
ALIXE
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spelling ALIXE: A phase-combination tool for fragment-based molecular replacementMillán, ClaudiaJiménez, E.Schuster, A.Diederichs, K.Usón, IsabelPhasingARCIMBOLDOFragment-based molecular replacementCombinationALIXEFragment-based molecular replacement exploits the use of very accurate yet incomplete search models. In the case of the ARCIMBOLDO programs, consistent phase sets produced from the placement and refinement of fragments with Phaser can be combined in order to increase their signal before proceeding to the step of density modification and autotracing with SHELXE. The program ALIXE compares multiple phase sets, evaluating mean phase differences to determine their common origin, and subsequently produces sets of combined phases that group consistent solutions. In this work, its use on different scenarios of very partial molecular-replacement solutions and its performance after the development of a much-optimized set of algorithms are described. The program is available both standalone and integrated within the ARCIMBOLDO programs. ALIXE has been analysed to identify its rate-limiting steps while exploring the best parameterization to improve its performance and make this software efficient enough to work on modest hardware. The algorithm has been parallelized and redesigned to meet the typical landscape of solutions. Analysis of pairwise correlation between the phase sets has also been explored to test whether this would provide additional insight. ALIXE can be used to exhaustively analyse all partial solutions produced or to complement those already selected for expansion, and also to reduce the number of redundant solutions, which is particularly relevant to the case of coiled coils, or to combine partial solutions from different programs. In each case parallelization and optimization to provide speedup makes its use amenable to typical hardware found in crystallography.CM is grateful to MICINN for her BES-2015-071397 scholarship associated with the Structural Biology Maria de Maeztu Unit of Excellence. This work was supported by grants BIO2015-64216-P, PGC2018-101370-B-100 and MDM2014-0435-01 from the Spanish Ministry of Economy and Competitiveness and 2017SGR-1192 from Generalitat de Catalunya.International Union of CrystallographyMinisterio de Economía y Competitividad (España)Generalitat de CatalunyaConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2020202020202020info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/223038reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/MDM-2014-0435-01info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BIO2015-64216-Phttp://dx.doi.org/10.1107/S205979832000056XSíinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2230382026-05-22T06:33:51Z
dc.title.none.fl_str_mv ALIXE: A phase-combination tool for fragment-based molecular replacement
title ALIXE: A phase-combination tool for fragment-based molecular replacement
spellingShingle ALIXE: A phase-combination tool for fragment-based molecular replacement
Millán, Claudia
Phasing
ARCIMBOLDO
Fragment-based molecular replacement
Combination
ALIXE
title_short ALIXE: A phase-combination tool for fragment-based molecular replacement
title_full ALIXE: A phase-combination tool for fragment-based molecular replacement
title_fullStr ALIXE: A phase-combination tool for fragment-based molecular replacement
title_full_unstemmed ALIXE: A phase-combination tool for fragment-based molecular replacement
title_sort ALIXE: A phase-combination tool for fragment-based molecular replacement
dc.creator.none.fl_str_mv Millán, Claudia
Jiménez, E.
Schuster, A.
Diederichs, K.
Usón, Isabel
author Millán, Claudia
author_facet Millán, Claudia
Jiménez, E.
Schuster, A.
Diederichs, K.
Usón, Isabel
author_role author
author2 Jiménez, E.
Schuster, A.
Diederichs, K.
Usón, Isabel
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Economía y Competitividad (España)
Generalitat de Catalunya
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Phasing
ARCIMBOLDO
Fragment-based molecular replacement
Combination
ALIXE
topic Phasing
ARCIMBOLDO
Fragment-based molecular replacement
Combination
ALIXE
description Fragment-based molecular replacement exploits the use of very accurate yet incomplete search models. In the case of the ARCIMBOLDO programs, consistent phase sets produced from the placement and refinement of fragments with Phaser can be combined in order to increase their signal before proceeding to the step of density modification and autotracing with SHELXE. The program ALIXE compares multiple phase sets, evaluating mean phase differences to determine their common origin, and subsequently produces sets of combined phases that group consistent solutions. In this work, its use on different scenarios of very partial molecular-replacement solutions and its performance after the development of a much-optimized set of algorithms are described. The program is available both standalone and integrated within the ARCIMBOLDO programs. ALIXE has been analysed to identify its rate-limiting steps while exploring the best parameterization to improve its performance and make this software efficient enough to work on modest hardware. The algorithm has been parallelized and redesigned to meet the typical landscape of solutions. Analysis of pairwise correlation between the phase sets has also been explored to test whether this would provide additional insight. ALIXE can be used to exhaustively analyse all partial solutions produced or to complement those already selected for expansion, and also to reduce the number of redundant solutions, which is particularly relevant to the case of coiled coils, or to combine partial solutions from different programs. In each case parallelization and optimization to provide speedup makes its use amenable to typical hardware found in crystallography.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020
2020
2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/223038
url http://hdl.handle.net/10261/223038
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/MDM-2014-0435-01
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BIO2015-64216-P
http://dx.doi.org/10.1107/S205979832000056X
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv International Union of Crystallography
publisher.none.fl_str_mv International Union of Crystallography
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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