Protocol

Structural Proteomics

Volume 426 of the series Methods in Molecular Biology™ pp 419-435

Automated Structure Solution with the PHENIX Suite

  • Peter H. ZwartAffiliated withLawrence Berkeley National Laboratory
  • , Pavel V. AfonineAffiliated withLawrence Berkeley National Laboratory
  • , Ralf W. Grosse-KunstleveAffiliated withLawrence Berkeley National Laboratory
  • , Li-Wei HungAffiliated withBiophysics Group, Los Alamos National Laboratory
  • , Thomas R. IoergerAffiliated withDepartment of Computer Science, Texas A&M University
  • , Airlie J. McCoyAffiliated withDepartment of Haematology, University of Cambridge, Cambridge Institute for Medical Research
  • , Erik McKeeAffiliated withDepartment of Computer Science, Texas A&M University
  • , Nigel W. MoriartyAffiliated withLawrence Berkeley National Laboratory
  • , Randy J. ReadAffiliated withDepartment of Haematology, University of Cambridge, Cambridge Institute for Medical Research
    • , James C. SacchettiniAffiliated withDepartment of Biochemistry and Biophysics, Texas A&M University
    • , Nicholas K. SauterAffiliated withLawrence Berkeley National Laboratory
    • , Laurent C. StoroniAffiliated withDepartment of Haematology, University of Cambridge, Cambridge Institute for Medical Research
    • , Thomas C. TerwilligerAffiliated withBiophysics Division, Los Alamos National Laboratory
    • , Paul D. AdamsAffiliated withBerkeley Structural Genomics Center, Lawrence Berkeley National Laboratory, and Department of Chemistry, University of California

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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.