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Automated Structure Solution with the PHENIX Suite

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Structural Proteomics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 426))

 

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.

Author information

Authors and Affiliations

  1. Lawrence Berkeley National Laboratory, Berkeley, California

    Peter H. Zwart, Pavel V. Afonine, Ralf W. Grosse-Kunstleve, Nigel W. Moriarty & Nicholas K. Sauter

  2. Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico

    Li-Wei Hung

  3. Department of Computer Science, Texas A&M University, College Hill, Texas

    Thomas R. Ioerger & Erik McKee

  4. Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom

    Airlie J. McCoy, Randy J. Read & Laurent C. Storoni

  5. Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas

    James C. Sacchettini

  6. Biophysics Division, Los Alamos National Laboratory, Los Alamos, New Mexico

    Thomas C. Terwilliger

  7. Berkeley Structural Genomics Center, Lawrence Berkeley National Laboratory, and Department of Chemistry, University of California, Berkeley, California

    Paul D. Adams

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  1. Peter H. Zwart
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  2. Pavel V. Afonine
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  9. Randy J. Read
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Editor information

Editors and Affiliations

  1. School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Queensland, Australia

    Bostjan Kobe

  2. School of Molecular and Microbial Biosciences, University of Sydney, Sydney, Australia

    Mitchell Guss

  3. School of Molecular and Microbial Sciences and Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia

    Thomas Huber

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© 2008 Humana Press, a part of Springer Science+Business Media, LLC

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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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  • DOI: https://doi.org/10.1007/978-1-60327-058-8_28

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-809-6

  • Online ISBN: 978-1-60327-058-8

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