Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1107/S2059798322009706 http://hdl.handle.net/11449/246300 |
Resumo: | Structure predictions have matched the accuracy of experimental structures from close homologues, providing suitable models for molecular replacement phasing. Even in predictions that present large differences due to the relative movement of domains or poorly predicted areas, very accurate regions tend to be present. These are suitable for successful fragment-based phasing as implemented in ARCIMBOLDO. The particularities of predicted models are inherently addressed in the new predicted_model mode, rendering preliminary treatment superfluous but also harmless. B-value conversion from predicted LDDT or error estimates, the removal of unstructured polypeptide, hierarchical decomposition of structural units from domains to local folds and systematically probing the model against the experimental data will ensure the optimal use of the model in phasing. Concomitantly, the exhaustive use of models and stereochemistry in phasing, refinement and validation raises the concern of crystallographic model bias and the need to critically establish the information contributed by the experiment. Therefore, in its predicted_model mode ARCIMBOLDO_SHREDDER will first determine whether the input model already constitutes a solution or provides a straightforward solution with Phaser. If not, extracted fragments will be located. If the landscape of solutions reveals numerous, clearly discriminated and consistent probes or if the input model already constitutes a solution, model-free verification will be activated. Expansions with SHELXE will omit the partial solution seeding phases and all traces outside their respective masks will be combined in ALIXE, as far as consistent. This procedure completely eliminates the molecular replacement search model in favour of the inferences derived from this model. In the case of fragments, an incorrect starting hypothesis impedes expansion. The predicted_model mode has been tested in different scenarios. |
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Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDERAlphaFoldARCIMBOLDOARCIMBOLDO_SHREDDERfragment-based molecular replacementmodel biasphasingpredictionsRoseTTAFoldverificationStructure predictions have matched the accuracy of experimental structures from close homologues, providing suitable models for molecular replacement phasing. Even in predictions that present large differences due to the relative movement of domains or poorly predicted areas, very accurate regions tend to be present. These are suitable for successful fragment-based phasing as implemented in ARCIMBOLDO. The particularities of predicted models are inherently addressed in the new predicted_model mode, rendering preliminary treatment superfluous but also harmless. B-value conversion from predicted LDDT or error estimates, the removal of unstructured polypeptide, hierarchical decomposition of structural units from domains to local folds and systematically probing the model against the experimental data will ensure the optimal use of the model in phasing. Concomitantly, the exhaustive use of models and stereochemistry in phasing, refinement and validation raises the concern of crystallographic model bias and the need to critically establish the information contributed by the experiment. Therefore, in its predicted_model mode ARCIMBOLDO_SHREDDER will first determine whether the input model already constitutes a solution or provides a straightforward solution with Phaser. If not, extracted fragments will be located. If the landscape of solutions reveals numerous, clearly discriminated and consistent probes or if the input model already constitutes a solution, model-free verification will be activated. Expansions with SHELXE will omit the partial solution seeding phases and all traces outside their respective masks will be combined in ALIXE, as far as consistent. This procedure completely eliminates the molecular replacement search model in favour of the inferences derived from this model. In the case of fragments, an incorrect starting hypothesis impedes expansion. The predicted_model mode has been tested in different scenarios.Science and Technology Facilities CouncilMinisterio de Ciencia e InnovaciónCrystallographic Methods Institute of Molecular Biology of Barcelona (IBMB-CSIC) Helix Building, Barcelona Science ParkBaldiri Reixac 15Department of Crystallography and Structural Biology Institute of Physical Chemistry `Rocasolano' Spanish National Research Council (CSIC)Department of Biophysics and Pharmacology Biosciences Institute São Paulo State University (UNESP)Department of Biophysics and Pharmacology Biosciences Institute São Paulo State University (UNESP)Science and Technology Facilities Council: Agreement for the integration of methods into the CCP4 software distribution, ARCIMBOLDO_LOWMinisterio de Ciencia e Innovación: BES-2017-080368Ministerio de Ciencia e Innovación: PGC2018-101370-B-100Ministerio de Ciencia e Innovación: PID2020-115331GB-I00Ministerio de Ciencia e Innovación: PRE2019-087953Helix BuildingSpanish National Research Council (CSIC)Universidade Estadual Paulista (UNESP)Medina, AnaJiménez, ElisabetCaballero, IracemaCastellví, AlbertTriviño Valls, JosepAlcorlo, MartinMolina, RafaelHermoso, Juan A.Sammito, Massimo D.Borges, Rafael [UNESP]Usón, Isabel2023-07-29T12:37:13Z2023-07-29T12:37:13Z2022-11-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article1283-1293http://dx.doi.org/10.1107/S2059798322009706Acta crystallographica. Section D, Structural biology, v. 78, p. 1283-1293.2059-7983http://hdl.handle.net/11449/24630010.1107/S20597983220097062-s2.0-85141889186Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengActa crystallographica. Section D, Structural biologyinfo:eu-repo/semantics/openAccess2023-07-29T12:37:13Zoai:repositorio.unesp.br:11449/246300Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T20:43:55.992602Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER |
title |
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER |
spellingShingle |
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER Medina, Ana AlphaFold ARCIMBOLDO ARCIMBOLDO_SHREDDER fragment-based molecular replacement model bias phasing predictions RoseTTAFold verification |
title_short |
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER |
title_full |
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER |
title_fullStr |
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER |
title_full_unstemmed |
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER |
title_sort |
Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER |
author |
Medina, Ana |
author_facet |
Medina, Ana Jiménez, Elisabet Caballero, Iracema Castellví, Albert Triviño Valls, Josep Alcorlo, Martin Molina, Rafael Hermoso, Juan A. Sammito, Massimo D. Borges, Rafael [UNESP] Usón, Isabel |
author_role |
author |
author2 |
Jiménez, Elisabet Caballero, Iracema Castellví, Albert Triviño Valls, Josep Alcorlo, Martin Molina, Rafael Hermoso, Juan A. Sammito, Massimo D. Borges, Rafael [UNESP] Usón, Isabel |
author2_role |
author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Helix Building Spanish National Research Council (CSIC) Universidade Estadual Paulista (UNESP) |
dc.contributor.author.fl_str_mv |
Medina, Ana Jiménez, Elisabet Caballero, Iracema Castellví, Albert Triviño Valls, Josep Alcorlo, Martin Molina, Rafael Hermoso, Juan A. Sammito, Massimo D. Borges, Rafael [UNESP] Usón, Isabel |
dc.subject.por.fl_str_mv |
AlphaFold ARCIMBOLDO ARCIMBOLDO_SHREDDER fragment-based molecular replacement model bias phasing predictions RoseTTAFold verification |
topic |
AlphaFold ARCIMBOLDO ARCIMBOLDO_SHREDDER fragment-based molecular replacement model bias phasing predictions RoseTTAFold verification |
description |
Structure predictions have matched the accuracy of experimental structures from close homologues, providing suitable models for molecular replacement phasing. Even in predictions that present large differences due to the relative movement of domains or poorly predicted areas, very accurate regions tend to be present. These are suitable for successful fragment-based phasing as implemented in ARCIMBOLDO. The particularities of predicted models are inherently addressed in the new predicted_model mode, rendering preliminary treatment superfluous but also harmless. B-value conversion from predicted LDDT or error estimates, the removal of unstructured polypeptide, hierarchical decomposition of structural units from domains to local folds and systematically probing the model against the experimental data will ensure the optimal use of the model in phasing. Concomitantly, the exhaustive use of models and stereochemistry in phasing, refinement and validation raises the concern of crystallographic model bias and the need to critically establish the information contributed by the experiment. Therefore, in its predicted_model mode ARCIMBOLDO_SHREDDER will first determine whether the input model already constitutes a solution or provides a straightforward solution with Phaser. If not, extracted fragments will be located. If the landscape of solutions reveals numerous, clearly discriminated and consistent probes or if the input model already constitutes a solution, model-free verification will be activated. Expansions with SHELXE will omit the partial solution seeding phases and all traces outside their respective masks will be combined in ALIXE, as far as consistent. This procedure completely eliminates the molecular replacement search model in favour of the inferences derived from this model. In the case of fragments, an incorrect starting hypothesis impedes expansion. The predicted_model mode has been tested in different scenarios. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-11-01 2023-07-29T12:37:13Z 2023-07-29T12:37:13Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1107/S2059798322009706 Acta crystallographica. Section D, Structural biology, v. 78, p. 1283-1293. 2059-7983 http://hdl.handle.net/11449/246300 10.1107/S2059798322009706 2-s2.0-85141889186 |
url |
http://dx.doi.org/10.1107/S2059798322009706 http://hdl.handle.net/11449/246300 |
identifier_str_mv |
Acta crystallographica. Section D, Structural biology, v. 78, p. 1283-1293. 2059-7983 10.1107/S2059798322009706 2-s2.0-85141889186 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Acta crystallographica. Section D, Structural biology |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
1283-1293 |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808129239447240704 |