KOPS - The Institutional Repository of the University of Konstanz

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

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

Cite This

Files in this item

Checksum: MD5:51c30cd5dd3fe2bd08ca7a579c92cafa

MILLÁN, Claudia, Elisabet JIMÉNEZ, Antonia SCHUSTER, Kay DIEDERICHS, Isabel USÓN, 2020. ALIXE : a phase-combination tool for fragment-based molecular replacement. In: Acta Crystallographica Section D : Structural Biology. International Union of Crystallography (IUCr). 76(3), pp. 209-220. ISSN 0907-4449. eISSN 2059-7983. Available under: doi: 10.1107/S205979832000056X

@article{Millan2020ALIXE-48941, title={ALIXE : a phase-combination tool for fragment-based molecular replacement}, year={2020}, doi={10.1107/S205979832000056X}, number={3}, volume={76}, issn={0907-4449}, journal={Acta Crystallographica Section D : Structural Biology}, pages={209--220}, author={Millán, Claudia and Jiménez, Elisabet and Schuster, Antonia and Diederichs, Kay and Usón, Isabel} }

<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:void="http://rdfs.org/ns/void#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/rdf/resource/123456789/48941"> <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/28"/> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2020-03-05T07:05:06Z</dcterms:available> <foaf:homepage rdf:resource="http://localhost:8080/jspui"/> <dc:rights>terms-of-use</dc:rights> <dc:creator>Jiménez, Elisabet</dc:creator> <dcterms:abstract xml:lang="eng">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. ARCIMBOLDO_BORGES and ARCIMBOLDO_SHREDDER now call on ALIXE by default.</dcterms:abstract> <dc:creator>Usón, Isabel</dc:creator> <dc:contributor>Schuster, Antonia</dc:contributor> <dcterms:rights rdf:resource="https://rightsstatements.org/page/InC/1.0/"/> <dc:contributor>Millán, Claudia</dc:contributor> <dcterms:title>ALIXE : a phase-combination tool for fragment-based molecular replacement</dcterms:title> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2020-03-05T07:05:06Z</dc:date> <dcterms:issued>2020</dcterms:issued> <dc:language>eng</dc:language> <dc:creator>Schuster, Antonia</dc:creator> <dc:contributor>Jiménez, Elisabet</dc:contributor> <dc:contributor>Usón, Isabel</dc:contributor> <dc:creator>Millán, Claudia</dc:creator> <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/48941"/> <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/48941/1/Millan_2-qg7nj9q92y156.pdf"/> <dc:contributor>Diederichs, Kay</dc:contributor> <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/28"/> <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/48941/1/Millan_2-qg7nj9q92y156.pdf"/> <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/> <dc:creator>Diederichs, Kay</dc:creator> </rdf:Description> </rdf:RDF>

Downloads since Mar 5, 2020 (Information about access statistics)

Millan_2-qg7nj9q92y156.pdf 78

This item appears in the following Collection(s)

Search KOPS


Browse

My Account