Pairwise running of automated crystallographic model-building pipelines

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)814-823
Number of pages10
JournalActa Crystallographica Section D: Structural Biology
Issue number9
Early online date19 Aug 2020
Publication statusPublished - 1 Sept 2020


  • model building
  • software
  • structure solution

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