PHENIX
PHENIX automates macromolecular structure determination using X-ray crystallography, neutron diffraction, electron cryo-microscopy, and related methods.
Key Features:
- Automation and Integration: Advanced algorithms reduce manual intervention and integrate computational tasks across data processing, model building, and refinement.
- Experimental Technique Support: Supports X-ray diffraction, neutron diffraction, and electron cryo-microscopy and is tailored to handle method-specific properties of experimental data.
- Structure Solution Workflow: Provides automated steps for initial data-quality assessment, model building, validation, rebuilding, refinement, and deposition.
- Repetitive-task Automation and Defaults: Automates repetitive procedures and applies default parameter settings to promote consistent, objective processing.
Scientific Applications:
- Structural Genomics: Enables high-throughput determination of protein structures from genomic sequences to populate protein structure databases.
- Molecular Mechanism Analysis: Produces macromolecular models used to investigate biological processes at the molecular level.
- Drug Discovery and Therapeutics: Provides accurate macromolecular structures that support structure-based drug design and therapeutic development.
Methodology:
Advanced algorithms perform automated data-quality assessment, model building, validation, rebuilding, refinement, and structure deposition while integrating computational tasks to minimize subjective input.
Topics
Collections
Details
- Cost:
- Free of charge
- Tool Type:
- workflow
- Operating Systems:
- Linux, Mac
- Programming Languages:
- Python
- Added:
- 2/16/2015
- Last Updated:
- 11/24/2024
Operations
Publications
Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung L, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. <i>PHENIX</i>: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica Section D Biological Crystallography. 2010;66(2):213-221. doi:10.1107/s0907444909052925. PMID:20124702. PMCID:PMC2815670.
Adams PD, Grosse-Kunstleve RW, Hung L, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC. <i>PHENIX</i>: building new software for automated crystallographic structure determination. Acta Crystallographica Section D Biological Crystallography. 2002;58(11):1948-1954. doi:10.1107/s0907444902016657. PMID:12393927.
Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung L, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in <i>Phenix</i>. Acta Crystallographica Section D Structural Biology. 2019;75(10):861-877. doi:10.1107/s2059798319011471. PMID:31588918. PMCID:PMC6778852.