Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

By T. C. Terwilliger, R. Grosse-Kunstleve, Pavel V. Afonine, Nigel W. Moriarty, Petrus H. Zwart, Li-Wei Hung, Randy J. Read, Paul D. Adams. 2007

450 citations recorded by the source corpus.

The highly automated PHENIX AutoBuild wizard is described. The procedure can be applied equally well to phases derived from isomorphous/anomalous and molecular-replacement methods.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. Paul D. Adams
2. Pavel V. Afonine
3. Randy J. Read
4. T. C. Terwilliger
5. A. McCoy
6. Nathaniel Echols
7. R. Grosse-Kunstleve
8. G. Bunkoczi

In Materials Chemistry

1. Paul D. Adams
2. Pavel V. Afonine
3. Randy J. Read
4. T. C. Terwilliger
5. Nathaniel Echols
6. David Baker
7. A. McCoy
8. G. Bunkoczi

In Molecular Biology

1. Paul D. Adams
2. Randy J. Read
3. T. C. Terwilliger
4. Pavel V. Afonine
5. David Baker
6. Nathaniel Echols
7. A. McCoy
8. G. Bunkoczi

Citations in the corpus

• Using SAD data in Phaser (2011, positive): “If the map is sufficient to build a partial preliminary model using a program such as ARP/ wARP (Langer et al., 2008), PHENIX AutoBuild (Terwilliger et al., 2008) or Buccaneer (Cowtan, 2006), then this model can be used to re-initiate substructure determination.”
• phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta (2012, methodology): “The top models (typically 2) are then rebuilt with phenix.autobuild [19] based on the crystallographic data and the sequence of the target macromolecule.”
• Structure of the decoy module of human glycoprotein 2 and uromodulin and its interaction with bacterial adhesin FimH (2022, methodology): “Cryo-EM single particle analysis averages independent particle observations, and – as reported in Supplementary Table 3 – Randomization X-ray crystallography: random assignment of reflections to working or free sets was automatically performed by PHENIX (P1 data) or XDS (P2(1)2(1)2(1) and C2 data).”
• New World Bats Harbor Diverse Influenza A Viruses (2013, methodology): “H18 HA exhibited no specific binding to a custom sialoside microarray (data not shown) [9,21] or the glycan microarray of the Consortium for Functional Glycomics (CFG) that contains 610 diverse glycans found on mammalian cells, including over 100 unique sialosides (a2-3, a2-6,, a2-8, and mixed linka”
• Recent developments in phasing and structure refinement for macromolecular crystallography (2009, methodology): “Adams PD, Grosse-Kunstleve RW, Hung L-W, Ioerger TR, McCoy AJ, Moriarty NW, Read RJ, Sacchettini JC, Sauter NK, Terwilliger TC: PHENIX, building new software for automated crystallographic structure determination.”
• Automated map sharpening by maximization of detail and connectivity (2018, methodology): “…determination (Terwilliger et al., 2009) by experimental phasing and the phenix.autobuild tool for iterative model-building, density modification and refinement (Terwilliger et al., 2008), the current default is to sharpen maps using an empirical formula based on the resolution of the map.”