Improvement of protein phases by coarse model modification

By Vladimir Y. Lunin, Alexandre Urzhumtsev. 1984

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Towards automated crystallographic structure refinement with phenix.refine (2012, background): “…(Pannu & Read, 1996; Bricogne & Irwin, 1996; Murshudov et al., 1997; Adams et al., 1997; Pannu et al., 1998) the calculation of the ML target (Lunin & Urzhumtsev, 1984; Read, 1986, 1990; Lunin & Skovoroda, 1995) requires an estimation of model error parameters, which depend on the current…”
Real-space refinement in PHENIX for cryo-EM and crystallography (2018, background): “…from the atomic model directly as a sum of individual contributions of M atoms with each contribution being a Fourier image (or its approximation) of the corresponding atom at a given resolution (e.g. Diamond, 1971; Lunin & Urzhumtsev, 1984; Chapman, 1995; Mooij et al., 2006; Sorzano et al., 2015).”
Likelihood-based refinement. I. Irremovable model errors. (2002, methodology): “A special type of this likelihood function, which was used primarily for the evaluation of model quality (Lunin & Urzhumtsev, 1984; Read, 1986, 1990; Lunin & Skovoroda, 1995; Urzhumtsev et al., 1996), was suggested recently as a new goal function for the re®nement of atomic models (Pannu & Read,…”
A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent. (2001, result): “A similar line of arguments could be used to show that maximum-likelihood re®nement (Lunin & Urzhumtsev, 1984; Read, 1986; Bricogne, 1988; Read, 1990; Carter et al., 1990; Murshudov et al., 1997) is similar to some extent to that of realspace re®nement (3).”
FEM: feature-enhanced map (2014, background): “(ii) Obtaining maps derived from ensembles of perturbed models or structure factors (Agarwal & Isaacs, 1977; Lunin & Urzhumtsev, 1984; Lunin et al., 1985; Baker et al., 1993; Perrakis et al., 1997; Rice et al., 1998; Reddy et al., 2003; Pražnikar et al., 2009; Lang et al., 2014).”
Pushing the boundaries of molecular replacement with maximum likelihood. (2001, methodology): “The program SIGMAA (Read, 1986) computes model phase probabilities using A parameters optimized by maximizing a likelihood function; Lunin & Urzhumtsev (1984) ®rst suggested estimating phase probabilities by maximizing a similar likelihood function.”