Electronic Reprint Biological Crystallography Iterative Model Building, Structure Refinement and Density Modification with the Phenix Autobuild Wizard Biological Crystallography Iterative Model…

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

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “AutoBuild (phenix.autobuild) is an automated system for model rebuilding and completion (Terwilliger et al., 2008).”
Improved Technologies Now Routinely Provide Protein NMR Structures Useful for Molecular Replacement (2011, background): “autobuild (Terwilliger et al., 2008) for automatic model rebuilding, which was less sensitive to low-resolution X-ray diffraction data.”
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps (2018, methodology): “More recent packages include phenix.autobuild (Terwilliger et al., 2008), which is distributed with the PHENIX suite (Adams et al., 2010), and Buccaneer (Cowtan, 2006), which is available via CCP4.”
Model morphing and sequence assignment after molecular replacement (2013, methodology): “The morphed model was then used as a starting point for creating an improved electron-density map by carrying out automated model building, density modification and refinement with phenix.autobuild (Terwilliger et al., 2008).”
Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum (2012, methodology): “First round of automated model building with AutoBuild Starting from the best DEN-refined structure, automated model building with AutoBuild (Terwilliger et al., 2008) was performed.”
Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. (2016, methodology): “Finally, phenix.autobuild (Terwilliger et al., 2008) is used for automatic model construction.”
The PDB_REDO server for macromolecular structure model optimization (2014, background): “…Keegan & Winn, 2007; Long et al., 2008; McCoy et al., 2007), density-map tracing and model building (e.g. Perrakis et al., 1999; Ioerger & Sacchettini, 2002; Cowtan, 2006; Terwilliger et al., 2008) and combinations thereof (e.g. Brunzelle et al., 2003; Holton & Alber, 2004; Kroemer et al., 2004).”
Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement (2014, methodology): “AutoBuild (Terwilliger, 2002; Terwilliger et al., 2008) model rebuilding was then performed using three different protocols: no NCS in model refinement, global (Cartesian-based) NCS as part of model refinement and torsion NCS with rotamer correction and consistency checks as part of model…”
FEM: feature-enhanced map (2014, unknown): “(iii) Various kinds of OMIT maps (Bhat & Cohen, 1984; Bhat, 1988; Hodel et al., 1992; Gunčar et al., 2000; Vellieux & Dijkstra, 1997; Terwilliger et al., 2008; Pražnikar et al., 2009; Cowtan, 2012).”
Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing (2016, methodology): “…techniques (Wang, 1985; Cowtan & Main, 1996; Abrahams & Leslie, 1996; Terwilliger, 2000; Cowtan, 2010) and interpreted in terms of an atomic model (see, for example, Jones et al., 1991; Perrakis et al., 1999; Emsley et al., 2010; Terwilliger et al., 2008; Cowtan, 2006; Langer et al., 2008).”