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 AutoBuildandSHELXE. 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 andR(free). In particular, runningPhenix AutoBuildafterBuccaneerimproved 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 runningPhenix AutoBuildon its own. In contrast,Phenix AutoBuildalone produced better structure completeness than the two pipelines combined for only 7% and 3% of these data sets.