Electronic Reprint Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination Biological Crystallography Phenix: Building New Software for…

By Paul D. Adams, R. Grosse-Kunstleve, Li-Wei Hung, Thomas R. Ioerger, A. McCoy, Nigel W. Moriarty, Randy J. Read, J. Sacchettini, Nicholas K. Sauter, T. C. Terwilliger

Subfields: Computational Biology & Bioinformatics, Software Engineering

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “Phenix Phenix (Adams et al., 2002, 2010) is a software suite that uses reduced data from X-ray diffraction, electron diffraction, neutron diffraction or cryo-EM to determine macromolecular structures.”
Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “The PDB format (Bernstein et al., 1977; Berman et al., 2000) is the most commonly used format for exchanging macromolecular model data and is therefore available as the input format for refinement in PHENIX.”
Features and development of Coot (2010, neutral): “Currently, suitable ﬁles are generated by the following software: Phaser (Storoni et al. , 2004), REFMAC (Murshudov et al. , 1997), phenix.reﬁne (Adams et al. , 2002), DM (Zhang et al. , 1997), Parrot (Cowtan, 2010), Pirate (Cowtan, 2000) and BUSTER (Blanc et al. , 2004).”
Phaser crystallographic software (2007, methodology): “Phaser source code has been distributed directly by the authors (see http://www-structmed.cimr.cam.ac.uk/phaser for details) and through the PHENIX and CCP4 (Collaborative Computing Project, Number 4, 1994) software suites.”
Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen (2017, methodology): “The structure was built manually in Coot (68) and refined using PHENIX (71).”
Improved estimates of coordinate error for molecular replacement (2013, methodology): “Phaser is available through the CCP4 (http://www.ccp4.ac.uk; Winn et al., 2011) and PHENIX (http://www.phenix-online.org; Adams et al., 2002) software distributions.”
Introduction to phasing (2010, methodology): “Similar methods are available in RESOLVE, particularly as part of the PHENIX suite of programs that cycle between phase improvement, model building and refinement (Adams et al., 2002).”
Structural basis for a bacterial Pip system plant effector recognition protein (2021, unknown): “P. D. Adams et al., PHENIX: Building new software for automated crystallographic structure determination.”
Neutron Crystal Structure of RAS GTPase Puts in Question the Protonation State of the GTP γ-Phosphate* (2015, methodology): “refine in the PHENIX suite of programs (43), and manual refinement was performed using COOT (44).”
Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice (2021, unknown): “Refinement of the complex was undertaken through iterative rounds of model building in COOT (71) and refinement in Phenix (76), with fourfold noncrystallographic symmetry restraints applied throughout.”
Structures of inactive CRP species reveal the atomic details of the allosteric transition that discriminates cyclic nucleotide second messengers. (2014, methodology): “Together with molecular replacement, SAD phasing was performed using AutoSol in PHENIX, with the anomalous coefficients f 0 = 8 and f 00 = 2.”