Maximum-likelihood density modification

By T. C. Terwilliger. 2000

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “D75, 861–877 Liebschner et al. Recent developments in Phenix 865 3 MAD, multiple-wavelength anomalous diffraction; MIR, multiple isomorphous replacement; SIR, single isomorphous replacement. ture Search; Grosse-Kunstleve & Adams, 2003; Bunkóczi et al., 2013), SOLVE (Terwilliger & Berendzen, 1999), ”
Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM (2020, methodology): “Densitymodification, iterative model-building and refinement procedures are then performed to improve the initial maps and phases (Cowtan & Zhang, 1999; Terwilliger, 2000, 2002; Terwilliger et al., 2008; Cowtan, 2010).”
Recent developments in phasing and structure refinement for macromolecular crystallography (2009, methodology): “Recently density modification procedures have been greatly improved through statistical treatments that reduce bias toward the starting map by solvent flipping [30] or maximum-likelihood techniques [31–33].”
Can I solve my structure by SAD phasing? Anomalous signal in SAD phasing (2016, methodology): “This electron-density map is normally then improved by density-modification 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.,…”
Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains. (2003, methodology): “Heavy atom sites (Se) were found with SOLVE at 3 Å (Terwilliger 2000).”
Conserved Neutralizing Epitope at Globular Head of Hemagglutinin in H3N2 Influenza Viruses (2014, methodology): “0-Å resolution, noncrystallographic symmetry (NCS) averaging between 12 molecules and B-factor sharpening brought dramatic map improvement up to atomic resolution level (41, 42).”
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): “…2010) and WHAT IF v.5.0 (Vriend, 1990); the agreement between the atomic model and the data using SFCHECK v.4.0 (Vaguine et al., 1999) and RESOLVE (Terwilliger, 2000); the protein sequence using ClustalW (Thompson et al., 1994); atom occupancies using MOLEMAN2 (Kleywegt, 2000) and the consistency…”
Inward-facing conformation of a multidrug resistance MATE family transporter (2019, methodology): “Density modification by RESOLVE (36) produced an electron density map at a resolution of 5.”
The closed structure of presequence protease PreP forms a unique 10 000 Å3 chamber for proteolysis (2006, methodology): “All 40 selenium atoms in the asymmetric unit were located by SHELXD (Schneider and Sheldrick, 2002) and phases were calculated and improved first with MLPHARE (Otwinowski, 1991) to confirm the solution and then with SOLVE (Terwilliger and Berendzen, 1999) and RESOLVE (Terwilliger, 2000) to create th”