Automated structure solution, density modification and model building.

By T. C. Terwilliger. 2002

324 citations recorded by the source corpus.

The approaches that form the basis of automated structure solution in SOLVE and RESOLVE are described. The use of a scoring scheme to convert decision making in macromolecular structure solution to an optimization problem has proven very useful and in many cases a single clear heavy-atom solution can be obtained and used for phasing. Statistical density modification is well suited to an automated approach to structure solution because the method is relatively insensitive to choices of numbers of cycles and solvent content. The detection of non-crystallographic symmetry (NCS) in heavy-atom sites and checking of potential NCS operations against the electron-density map has proven to be a reliable method for identification of NCS in most cases. Automated model building beginning with an FFT-based search for helices and sheets has been successful in automated model building for maps with resolutions as low as 3 A. The entire process can be carried out in a fully automatic fashion in many cases.

Subfields: Computational Theory and Mathematics, Materials Chemistry

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, neutral): “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), ”
Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation (2014, methodology): “Phases were calculated in Solve/Resolve (52), and the atomicmodel”
The Phenix Software for Automated Determination of Macromolecular Structures (2011, methodology): “…for structure determination, maximum-likelihood molecular replacement[6], heavy-atom search[18], template and pattern-based automated model-building[10, 19-21], automated macromolecular refinement[22], and iterative model-building, density modification and refinement that can operate at moderate…”
Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement (2014, methodology): “Thus, we recommend that models containing NCS-related chains which are solved by molecular replacement at sufficiently high resolution be rebuilt with AutoBuild with NCS refinement disabled to allow initial differences to be introduced prior to application of an appropriate refinement strategy for t”
Protonation‐mediated structural flexibility in the F conjugation regulatory protein, TraM (2006, methodology): “Automatic model building in RESOLVE (Terwilliger, 2002) placed 57 of the 68 ordered residues in the monomer.”
Introduction to phasing (2010, methodology): “These methods were originally encoded into programs such as DM (Cowtan & Zhang, 1999), RESOLVE (Terwilliger, 2002) and CNS (Brünger et al., 1998).”