Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

By T. C. Terwilliger, R. Grosse-Kunstleve, Pavel V. Afonine, Paul D. Adams, Nigel W. Moriarty, Petrus H. Zwart, Randy J. Read, D. Turk, Li-Wei Hung. 2007

51 citations recorded by the source corpus.

Heterogeneity in ensembles generated by independent model rebuilding principally reflects the limitations of the data and of the model-building process rather than the diversity of structures in the crystal.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Towards automated crystallographic structure refinement with phenix.refine (2012, background): “The variation of structures within the ensemble reflects two phenomena: refinement artifacts (limited convergence radius and speed) and (probably to a lesser degree) structural variability (Terwilliger et al., 2007).”
Alternate states of proteins revealed by detailed energy landscape mapping (2010, neutral): “NMR inadequately samples these loops, whereas new ensemble methods in crystallography 16,17 result Note that Rosetta's backbone is somewhat mobile, especially for Thr77, perhaps because stabilizing effects from the explicit water molecules and the crystal contact are not modeled.”
Interactive comparison and remediation of collections of macromolecular structures (2018, background): “33 It can be noted that there is often more than one indicator of a problem such as in the example discussing the ADPs, where problematic residues are also flagged as rotamer or Ramachandran outliers.”
Modelling dynamics in protein crystal structures by ensemble refinement (2012, unknown): “Multi-conformer structures represent both anisotropic and anharmonic disorder, but despite numerous attempts at automating the inclusion of minor conformations (DePristo et al., 2004; Levin et al., 2007; Terwilliger et al., 2007; Korostelev et al., 2009; van den Bedem et al., 2009; Lang et al., 2010”