A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent.

By Thomas J. Oldfield. 2001

61 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “The backbone dihedral angles can be restrained to stay in the allowed regions of the Ramachandran plot (Oldfield, 2001; Emsley et al., 2010; Headd et al., 2012).”
Towards automated crystallographic structure refinement with phenix.refine (2012, background): “…(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 et al.,…”
Real-space refinement in PHENIX for cryo-EM and crystallography (2018, methodology): “…tasks allow optimization using simulated annealing (SA; Brunger et al., 1987), morphing (Terwilliger at al., 2013), rigid-body refinement (see Afonine et al., 2009 and references within) and systematic residue side-chain optimizations using grid searches in torsion χ-angle space (Oldfield, 2001).”
Q|R: quantum-based refinement. (2017, methodology): “To address these problems, additional restraints have been used to augment (2) (see, for example, Oldfield, 2001; Echols et al., 2010; Headd et al., 2012; Sobolev et al., 2015), Trestraints plus ¼ Trestraints þ TSS þ TRamachandran þ Trotamer þ Treference: ð3Þ Here, TSS represents…”
Knowledge-based real-space explorations for low-resolution structure determination. (2006, background): “O (Jones and Kjeldgaard, 1997) and QUANTA ( Oldfield, 2001 ) first trace a Ca skeleton through the density with three-dimensional pattern recognition (Greer, 1974).”
Ligand placement based on prior structures: the guided ligand-replacement method (2013, methodology): “As a step towards automation, from within QUANTA, X-LIGAND (Oldfield, 2001b) could be used to automatically fit ligands with some success, albeit slowly for flexible ligands and still through an interactive session.”
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution (2012, unknown): “We have also implemented the target function described in Oldfield (2001), which uses simple ’, -based distance restraints to direct outliers to the nearest allowed region.”