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  • 1
    Electronic Resource
    Electronic Resource
    Eigensystem analysis of the refinement of a small metalloprotein (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 842-856 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The eigenvalues and eigenvectors of the least-squares normal matrix for the full-matrix refinement problem contain a great deal of information about the quality of a model; in particular the precision of the model parameters and correlations between those parameters. They also allow the isolation of those parameters or combinations of parameters which are not determined by the available data. Since a protein refinement is usually under-determined without the application of geometric restraints, such indicators of the reliability of a model offer an important contribution to structural knowledge. Eigensystem analysis is applied to the normal matrices for the refinement of a small metalloprotein using two data sets and models determined at different resolutions. The eigenvalue spectra reveal considerable information about the conditioning of the problem as the resolution varies. In the case of a restrained refinement, it also provides information about the impact of various restraints on the refinement. Initial results support conclusions drawn from the free R factor. Examination of the eigenvectors provides information about which regions of the model are poorly determined. In the case of a restrained refinement, it is also possible to isolate places where X-ray and geometric restraints are in disagreement, usually indicating a problem in the model.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900004856
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  • 2
    Electronic Resource
    Electronic Resource
    Error estimation and bias correction in phase-improvement calculations (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1555-1567 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: With the rise of Bayesian methods in crystallography, the error estimates attached to estimated phases are becoming as important as the phase estimates themselves. Phase improvement by density modification can cause problems in this environment because the quality of the resulting phases is usually overestimated. This problem is addressed by an extension of the γ correction [Abrahams (1997). Acta Cryst. D53, 371–376] to arbitrary density-modification techniques. The degree to which the improved phases are biased by the features of the initial map is investigated in order to determine the limits of the resulting procedure and the quality of the phase-error estimates.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444999007416
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  • 3
    Electronic Resource
    Electronic Resource
    General quadratic functions in real and reciprocal space and their application to likelihood phasing (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1612-1621 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A general multivariate quadratic function of the structure factors is constructed and transformed to obtain a quadratic function of the continuous electron density. Two special cases, where structure factors are independent and where electron-density values are independent, are examined. These results are related to the new likelihood-based framework of Terwilliger [Terwilliger (1999), Acta Cryst. D55, pp. 1863–1871] for employing structural information which was previously exploited by means of conventional density-modification calculations. The treatment here involves different assumptions and highlights new features of Terwilliger's calculation. The generalization quadratic construction allows the generation of cross terms relating all reflections and electron densities. Other applications of this approach are considered.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900013263
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  • 4
    Electronic Resource
    Electronic Resource
    Fast Fourier feature recognition (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1435-1444 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Various approaches have been demonstrated for the automatic interpretation of crystallographic data in terms of atomic models. The use of a masked Fourier-based search function has some benefits for this task. The application and optimization of this procedure is discussed in detail. The search function also acquires a statistical significance when used with an appropriate electron-density target and weighting, giving rise to improved results at low resolutions. Methods are discussed for building a library of protein fragments suitable for use with this procedure. These methods are demonstrated with the construction of a statistical target for the identification of short helical fragments in the electron density.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901010812
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  • 5
    Electronic Resource
    Electronic Resource
    Molecular replacement and its relatives (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1-1 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901014056
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  • 6
    Electronic Resource
    Electronic Resource
    Miscellaneous Algorithms for Density Modification (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 487-493 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Various algorithms are described, developed for the dm density modification package, which have not been described elsewhere. Methods are described for the following problems: determination of the absolute scale and overall temperature factor of a data set, by a method which is less dependent on data resolution than Wilson statistics; an efficient interpolation algorithm for averaging and its application to refinement of averaging operators; a method for the automatic determination of averaging masks.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444997011980
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  • 7
    Electronic Resource
    Electronic Resource
    Modified Phased Translation Functions and their Application to Molecular-Fragment Location (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 750-756 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Direct methods at high resolution have depended on the resolution of atomic like features in the map. At data resolutions more typical for protein structures (2–3 Å) individual atoms may not be resolved, so larger features must be identified. At one extreme the whole molecule may be located using the diffraction magnitudes alone by the molecular-replacement method. At the other extreme it is possible to locate individual residues in a well phased map. In this paper an intermediate problem is addressed: the location of multi-residue fragments on the basis of weak phase information. An agreement function based on the mean-squared difference between model and map over a masked region is shown to be more effective than a simple overlap integral, and may be efficiently calculated by Fourier methods. The techniques are compared using poorly phased electron-density maps at ∼3 Å for the proteins RNAse and O6-methylguanine-DNA-methyltransferase.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444997016247
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  • 8
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    Stay Out of Scientists' E-mails (2017)
    Springer Nature
    Details
    Publication Date: 2017-03-14
    Print ISSN: 0036-8733
    Electronic ISSN: 1946-7087
    Topics: Biology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 9
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    Erratum: Carbohydrate anomalies in the PDB (2015)
    Springer Nature
    Details
    Publication Date: 2015-06-17
    Print ISSN: 1552-4450
    Electronic ISSN: 1552-4469
    Topics: Biology , Chemistry and Pharmacology
    Published by Springer Nature
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  • 10
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    Carbohydrate anomalies in the PDB (2015)
    Springer Nature
    Details
    Publication Date: 2015-04-17
    Print ISSN: 1552-4450
    Electronic ISSN: 1552-4469
    Topics: Biology , Chemistry and Pharmacology
    Published by Springer Nature
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