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International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 21.1, pp. 503-504
Section 21.1.7.2.7. Miscellaneous
aDepartment of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden |
Many other coordinate-based methods for assessing the validity or correctness of protein models have been developed. These include the profile method of Eisenberg and co-workers (Bowie et al., 1991![[link]](/graphics/greenarr.gif)
; Lüthy et al., 1992), the inspection of atomic volumes (Pontius et al., 1996), and the use of threading and other potentials (Sippl, 1993; Melo & Feytmans, 1998; Maiorov & Abagyan, 1998). Some of these methods are described in more detail elsewhere in this volume. The program WHAT IF (Vriend, 1990) contains a large array of quality checks, many of which are not available in other programs, that span the spectrum from administrative checks to global quality indicators (Hooft et al., 1996). During the refinement process, coordinate shifts can be used as a rough indication of `quality' or, rather, convergence (Carson et al., 1994; Kleywegt & Jones, 1996a). Crude models tend to undergo much larger changes during refinement than models that are essentially correct and complete. Also at the residue level, large coordinate shifts indicate residues that are worth a closer look.
Laskowski et al. (1994) have formulated single-number geometrical quality criteria, which they dubbed `G factors' in analogy to crystallographic R values. These G factors combine the results of a number of quality checks (covalent geometry, main-chain and side-chain torsion angles etc.) in a single number.
References
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