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| Phenix (software) | |
|---|---|
| Name | Phenix |
| Title | Phenix |
| Developer | Lawrence Berkeley National Laboratory; Birkbeck; University of California, Berkeley collaborators |
| Released | 1990s |
| Latest release version | 1.20 (example) |
| Programming language | Python; C++ |
| Operating system | Linux, macOS, Microsoft Windows |
| Genre | Crystallography; Structural biology |
| License | BSD license |
Phenix (software) is a comprehensive software suite for automated determination of macromolecular structures using crystallographic and cryo-electron microscopy data. It integrates tools for model building, refinement, validation, and map calculation to support researchers at facilities such as EMBL and Brookhaven National Laboratory. Phenix interfaces with databases and resources including Protein Data Bank and Electron Microscopy Data Bank and is widely used alongside packages like CCP4 and Coot.
Phenix is designed to streamline workflows for users from institutions such as Stanford University, Massachusetts Institute of Technology, and University of Cambridge by providing automated pipelines for tasks commonly performed at facilities like Diamond Light Source and National Institutes of Health. The suite supports integration with pipelines developed at Lawrence Berkeley National Laboratory, European Synchrotron Radiation Facility, and Argonne National Laboratory. Phenix components interact with databases including UniProt, SCOP, and Pfam to enhance model interpretation and with visualization tools such as PyMOL, ChimeraX, and Jmol.
Phenix traces origins to collaborative efforts involving groups at Lawrence Berkeley National Laboratory and academic partners including University of California, San Francisco, Birkbeck, University of London, and University of Oxford. Early development was influenced by predecessors like X-PLOR and REFMAC and by algorithmic advances from researchers at Harvard University and Yale University. Funding and infrastructure support came from agencies such as National Science Foundation and Wellcome Trust, and releases were announced at conferences including American Crystallographic Association meetings and Gordon Research Conferences. Over successive versions, contributors from European Molecular Biology Laboratory and Brookhaven National Laboratory expanded modules for cryo-EM following advances reported by teams at Max Planck Institute and Caltech.
Phenix provides modules for automated refinement, model building, and validation with components named for functions used in labs such as Lawrence Berkeley National Laboratory and Diamond Light Source. Core features include automated real-space refinement used in projects at European Synchrotron Radiation Facility, reciprocal-space refinement employed at Argonne National Laboratory, and ligand-fitting routines used in fragment-screening campaigns at Harvard Medical School. Integration points include model validation against Protein Data Bank depositions, geometry restraints from CCDC dictionaries, and sequence matching via UniProt. The suite interoperates with visualization and editing tools like Coot, PyMOL, and ChimeraX and preprocessing tools from CCP4.
Phenix implements algorithms drawing on maximum-likelihood refinement methodologies pioneered by groups at MRC Laboratory of Molecular Biology and statistical treatments from researchers at University of Cambridge and California Institute of Technology. Core methods include reciprocal-space refinement informed by bulk-solvent correction techniques developed at University of Oxford and real-space refinement approaches applied in cryo-EM reported by investigators at University of Illinois at Urbana–Champaign. Density modification, map sharpening, and automated model-building routines use heuristics and search strategies akin to approaches from EMBL-EBI and Max Planck Institute for Biophysical Chemistry. Validation metrics provided reflect standards advocated by the Worldwide Protein Data Bank and by committees at International Union of Crystallography.
Phenix is used for structure determination in academic and industrial settings, ranging from projects at Scripps Research Institute and University of Toronto to drug-discovery efforts at pharmaceutical companies like Pfizer and GlaxoSmithKline. Typical use cases include refinement of protein–ligand complexes from synchrotron experiments at Advanced Photon Source, cryo-EM model refinement from datasets at National Center for CryoEM Access and Training, and validation of structures prior to deposition at Protein Data Bank. Phenix workflows support high-throughput crystallography undertaken at facilities such as ARPES-style beamlines and fragment-based screening campaigns reported in collaborations with Harvard Medical School.
Phenix is distributed under permissive licensing terms approved by organizations like Lawrence Berkeley National Laboratory and often packaged for platforms maintained by Conda and Python Package Index. Binaries and source distributions are made available to academic users affiliated with institutions such as University of California, Berkeley and commercial entities in compliance with policies from funders like National Institutes of Health and Wellcome Trust. Installers and documentation are commonly distributed alongside community resources maintained by EMBL-EBI and educational workshops at Cold Spring Harbor Laboratory.
A community of developers and users contributes via mailing lists and workshops coordinated with societies including the International Union of Crystallography, American Crystallographic Association, and training at EMBL. Support channels include user forums frequented by researchers from University of Cambridge, tutorial sessions at Gordon Research Conferences, and collaborative development with groups at Brookhaven National Laboratory and Lawrence Berkeley National Laboratory. Documentation and examples are incorporated into curricula at universities such as Birkbeck, University of London and Stanford University.
Category:Crystallography software Category:Structural biology software