Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution, and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution, and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template- and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix. refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.
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Acknowledgments
PHENIX can be downloaded from http://www.phenix.online.org, and is freely available to nonprofit researchers. The open source crystallographic library (the CCTBX) is available from http://cctbx.sourceforge.net/.
The authors gratefully acknowledge the financial support of NIH/NIGMS through grants 5P01GM063210, 5P50GM062412, 5R01GM071939, and the PHENIX industrial consortium. This work was supported in part by the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
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Zwart, P.H. et al. (2008). Automated Structure Solution with the PHENIX Suite. In: Kobe, B., Guss, M., Huber, T. (eds) Structural Proteomics. Methods in Molecular Biology™, vol 426. Humana Press. https://doi.org/10.1007/978-1-60327-058-8_28
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