Pairwise running of automated crystallographic model-building pipelines

TY - JOUR

T1 - Pairwise running of automated crystallographic model-building pipelines

AU - Alharbi, Emad

AU - Calinescu, Radu

AU - Cowtan, Kevin

PY - 2020/9/1

Y1 - 2020/9/1

N2 - 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.

AB - 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.

KW - model building

KW - software

KW - structure solution

UR - http://www.scopus.com/inward/record.url?scp=85090178891&partnerID=8YFLogxK

U2 - 10.1107/S2059798320010542

DO - 10.1107/S2059798320010542

M3 - Article

C2 - 32876057

AN - SCOPUS:85090178891

SN - 2059-7983

VL - 76

SP - 814

EP - 823

JO - Acta Crystallographica Section D: Structural Biology

JF - Acta Crystallographica Section D: Structural Biology

IS - 9

ER -