The Phenix Software for Automated Determination of Macromolecular Structures

By Paul D. Adams, Pavel V. Afonine, G. Bunkoczi, Vincent B. Chen, Nathaniel Echols, J. Headd, Li-Wei Hung, Swati Jain, Gary J. Kapral, Ralf W Grosse Kunstleve and 8 more. Methods, 2011

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X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favour of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/016d3bdc18c895c45156deec86237a504c7954a9

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Citations in the corpus

OpenStructure: an integrated software framework for computational structural biology (2013, background): “In fact, this approach to multi-language computing has found favour with many in the scientific computing community (Schroeder et al., 2004; Kohlbacher & Lenhof, 2000; Adams et al., 2011) and Python has established itself as the de facto standard scripting language for scientific frameworks.”
Structural Basis for the Inhibition of the RNA-Dependent RNA Polymerase from SARS-CoV-2 by Remdesivir (2020, methodology): “The model was docked in the using Chimera(39) , followed by iterative manual adjustment in COOT (40) , real space refinement using real_space_refine in PHENIX (41) .”
An editor for the generation and customization of geometry restraints (2017, methodology): “Within the PHENIX package (Adams et al., 2010, 2011), chemical restraint generation is performed using the electronic Ligand Builder and Optimization Workbench (Moriarty et al., 2009).”
Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase (2020, methodology): “…to a resolution of 2.0 Å, an initial model was generated by MR phasing using the 1.9 Å XFEL structure (PDB entry 5k2d) modified to a polyalanine model, as the search model in the Phaser MR module [Phenix version 1.17 (McCoy et al., 2007)] in order to reduce phase bias (Adams et al., 2010, 2011).”