International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

International Tables for Crystallography (2006). Vol. F. ch. 21.1, p. 503   | 1 | 2 |

Section 21.1.7.2.3. Cα-only models

G. J. Kleywegta*

aDepartment of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
Correspondence e-mail: gerard@xray.bmc.uu.se

21.1.7.2.3. Cα-only models

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Validation of Cα-only models may be necessary if such a model is retrieved from the PDB to be used in molecular replacement or homology modelling exercises; however, not many validation tools can handle such models (Kleywegt, 1997[link]). The Cα backbone can be characterized by Cα—Cα distances (∼2.9 Å for a cis-peptide and ∼3.8 Å for a trans-peptide), Cα—Cα—Cα pseudo-angles and Cα—Cα—Cα—Cα pseudo-torsion angles (Kleywegt, 1997[link]). The pseudo-angles and torsion angles turn out to assume certain preferred value combinations (Oldfield & Hubbard, 1994[link]), much like the backbone ϕ and ψ torsions, and this can be employed for the validation of Cα-only models (Kleywegt, 1997[link]). In addition to these straightforward methods, the mean-field approach of Sippl (1993[link]) is also applicable to Cα-only models.

References

First citation Kleywegt, G. J. (1997). Validation of protein models from Cα coordinates alone. J. Mol. Biol. 273, 371–376.Google Scholar
First citation Oldfield, T. J. & Hubbard, R. E. (1994). Analysis of Cα geometry in protein structures. Proteins Struct. Funct. Genet. 18, 324–337.Google Scholar
First citation Sippl, M. J. (1993). Recognition of errors in three-dimensional structures of proteins. Proteins Struct. Funct. Genet. 17, 355–362.Google Scholar








































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