Improved methods for building protein models in electron density maps and the location of errors in these models.

By T. Jones, J. Zou, S. Cowan, M. Kjeldgaard, Serge HAGgGE. 1991

Subfields: Computational Biology & Bioinformatics

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “One measure of agreement between a model and a map is the model–map correlation coefficient (map CC; Brändén & Jones, 1990; Jones et al., 1991).”
Towards automated crystallographic structure refinement with phenix.refine (2012, background): “Real-space refinement (RSR) of coordinates has a long history (Diamond, 1971; Deisenhofer et al., 1985; Urzhumtsev, Lunin & Vernoslova, 1989; Jones et al., 1991; Oldfield, 2001; Chapman, 1995; see also the discussion of and references to earlier original works in Murshudov et al., 1997; Korostelev…”
Features and development of Coot (2010, neutral): “:3) about the vector joining the bounding C (cid:2) atoms (Jones et al. , 1991).”
The Buccaneer software for automated model building. 1. Tracing protein chains. (2006, background): “The skeleton is then interpreted in terms of C positions, which commonly occur near branch points in the skeleton (Jones et al., 1991).”
REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. (2004, methodology): “This aspect of the utilization of the available information is growing rapidly and there are already some applications of it in such branches of crystal structure analysis as model building (Jones et al., 1991) and density modi®cation (Terwilliger, 2003).”
BALBES: a molecular-replacement pipeline (2007, methodology): “The application of information derived from the PDB for molecular replacement, phase improvement (Terwilliger & Berendzen, 1999) and model building (Emsley & Cowtan, 2004; Jones et al., 1991) now routinely takes place.”
Coot: model-building tools for molecular graphics. (2004, background): “The introduction of FRODO (Jones, 1978) and then O (Jones et al., 1991) to the ®eld of protein crystallography was in each case revolutionary, each in their time breaking new ground in demonstrating what was possible with the current hardware.”
Crystal structure of mammalian α1,6-fucosyltransferase, FUT8 (2007, methodology): “The resultant experimental map using native1 data was traced and the model building was performed with the program O (Jones et al. 1991).”
Rules for nuclear localization sequence recognition by karyopherin beta 2. (2006, unknown): “A model comprising 90% of Kapβ2 was built using O (Jones et al., 1991), but electron density for the substrate remained uninterpretable even though M9NLS residue M276 could be clearly placed using a selenium site.”
Structure of the C‐terminal laminin G‐like domain pair of the laminin α2 chain harbouring binding sites for α‐dystroglycan and heparin (2000, methodology): “with O (Jones et al., 1991) and combination of model and SIR phases allowed the model to be completed.”
Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 (2008, methodology): “Crystallographic model building has been traditionally done by expert users, with the aid of specialized interactive graphics software such as”
Structural basis for inhibition of the epidermal growth factor receptor by cetuximab. (2005, methodology): “Following several rounds of model building using O (Jones et al., 1991 ) and refinement using CNS (Brunger et al., 1998), Protein expression and purification interpretable density for the remaining portions of sEGFR (C-terminal part sEGFR was produced and purified from baculovirus-infected Sf9…”