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Pairwise running of automated crystallographic model-building pipelines

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JournalActa Crystallographica Section D: Structural Biology
DateAccepted/In press - 31 Jul 2020
DateE-pub ahead of print - 19 Aug 2020
DatePublished (current) - 1 Sep 2020
Issue number9
Volume76
Number of pages10
Pages (from-to)814-823
Early online date19/08/20
Original languageEnglish

Abstract

For the last two decades, researchers have worked independently to automate protein model building, and four widely used software pipelines have been developed for this purpose: ARP/wARP, Buccaneer, Phenix AutoBuild and SHELXE. Here, the usefulness of combining these pipelines to improve the built protein structures by running them in pairwise combinations is examined. The results show that integrating these pipelines can lead to significant improvements in structure completeness and Rfree. In particular, running Phenix AutoBuild after Buccaneer improved structure completeness for 29% and 75% of the data sets that were examined at the original resolution and at a simulated lower resolution, respectively, compared with running Phenix AutoBuild on its own. In contrast, Phenix AutoBuild alone produced better structure completeness than the two pipelines combined for only 7% and 3% of these data sets.

    Research areas

  • model building, software, structure solution

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