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Article: IPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination

TitleIPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination
Authors
KeywordsOASIS
IPCAS
direct methods
protein crystallography
single-particle cryo-EM image processing
Issue Date2020
PublisherInternational Union of Crystallography. The Journal's web site is located at http://journals.iucr.org/j/journalhomepage.html
Citation
Journal of Applied Crystallography, 2020, v. 53, p. 253-261 How to Cite?
AbstractA new version (2.0) of the pipeline IPCAS (Iterative Protein Crystal structure Automatic Solution) has been released, in which the program OASIS performs direct-method single-wavelength anomalous diffraction/single isomorphous replacement phasing and direct-method-aided partial-structure extension. IPCAS incorporates the widely used packages CCP4 and PHENIX for locating heavy atoms, density modification, molecular replacement, model building and refinement. Important extensions to the previous version of IPCAS include a resolution screening method for non-crystallographic symmetry searching, an alternate model-building protocol for avoiding premature convergence and direct-method image processing for electron microscopy maps, including single-particle cryo-EM maps. Moreover, a new graphical user interface is provided for controlling and real-time monitoring of the whole dual-space iterative process, which works as a plugin to CCP4i. Applications of the new IPCAS to difficult cases have yielded promising results, including `direct-method phasing and fragment extension' from weak anomalous diffraction signal data and `direct-method-aided partial-structure extension' from low-homology models.
Persistent Identifierhttp://hdl.handle.net/10722/288396
ISSN
2019 Impact Factor: 2.995
2015 SCImago Journal Rankings: 2.373

 

DC FieldValueLanguage
dc.contributor.authorDing, W-
dc.contributor.authorZhang, T-
dc.contributor.authorHe, Y-
dc.contributor.authorWang, J-
dc.contributor.authorWu, L-
dc.contributor.authorHan, P-
dc.contributor.authorZheng, C-
dc.contributor.authorGu, Y-
dc.contributor.authorZENG, L-
dc.contributor.authorHao, Q-
dc.contributor.authorFan, H-
dc.date.accessioned2020-10-05T12:12:16Z-
dc.date.available2020-10-05T12:12:16Z-
dc.date.issued2020-
dc.identifier.citationJournal of Applied Crystallography, 2020, v. 53, p. 253-261-
dc.identifier.issn0021-8898-
dc.identifier.urihttp://hdl.handle.net/10722/288396-
dc.description.abstractA new version (2.0) of the pipeline IPCAS (Iterative Protein Crystal structure Automatic Solution) has been released, in which the program OASIS performs direct-method single-wavelength anomalous diffraction/single isomorphous replacement phasing and direct-method-aided partial-structure extension. IPCAS incorporates the widely used packages CCP4 and PHENIX for locating heavy atoms, density modification, molecular replacement, model building and refinement. Important extensions to the previous version of IPCAS include a resolution screening method for non-crystallographic symmetry searching, an alternate model-building protocol for avoiding premature convergence and direct-method image processing for electron microscopy maps, including single-particle cryo-EM maps. Moreover, a new graphical user interface is provided for controlling and real-time monitoring of the whole dual-space iterative process, which works as a plugin to CCP4i. Applications of the new IPCAS to difficult cases have yielded promising results, including `direct-method phasing and fragment extension' from weak anomalous diffraction signal data and `direct-method-aided partial-structure extension' from low-homology models.-
dc.languageeng-
dc.publisherInternational Union of Crystallography. The Journal's web site is located at http://journals.iucr.org/j/journalhomepage.html-
dc.relation.ispartofJournal of Applied Crystallography-
dc.subjectOASIS-
dc.subjectIPCAS-
dc.subjectdirect methods-
dc.subjectprotein crystallography-
dc.subjectsingle-particle cryo-EM image processing-
dc.titleIPCAS: a direct-method-based pipeline from phasing to model building and refinement for macromolecular structure determination-
dc.typeArticle-
dc.identifier.emailHao, Q: qhao@hku.hk-
dc.identifier.authorityHao, Q=rp01332-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1107/S1600576719015115-
dc.identifier.scopuseid_2-s2.0-85077698178-
dc.identifier.hkuros315240-
dc.identifier.volume53-
dc.identifier.spage253-
dc.identifier.epage261-
dc.publisher.placeUnited Kingdom-

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