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  • 1
    Electronic Resource
    Electronic Resource
    Critical evaluation of comparative model building of Streptomyces griseus trypsin (1984)
    s.l. : American Chemical Society
    Biochemistry 23 (1984), S. 6570-6575 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00321a045
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  • 2
    Electronic Resource
    Electronic Resource
    Structure of the complex of Streptomyces griseus protease B and the third domain of the turkey ovomucoid inhibitor at 1.8-.ANG. resolution (1983)
    s.l. : American Chemical Society
    Biochemistry 22 (1983), S. 4420-4433 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00288a012
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  • 3
    Electronic Resource
    Electronic Resource
    Comparison of the B-pentamers of heat-labile enterotoxin and verotoxin-1: two structures with remarkable similarity and dissimilarity (1993)
    s.l. : American Chemical Society
    Biochemistry 32 (1993), S. 191-198 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00052a025
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  • 4
    Electronic Resource
    Electronic Resource
    Crystal and molecular structure of [tris(4,5-diisopropylimidazol-2-yl)phosphine]dichlorozinc(II)-bis[N,N-dimethylformamide] (1981)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 103 (1981), S. 6947-6952 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00413a030
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  • 5
    Electronic Resource
    Electronic Resource
    Phenylalanine 30 plays an important role in receptor binding of verotoxin-1 (1996)
    Oxford BSL : Blackwell Science Ltd
    Molecular microbiology 19 (1996), S. 0 
    Details
    ISSN: 1365-2958
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: The homopentameric B subunit of verotoxin 1 (VT1) binds to the glycosphingolipid receptor globotriaosylceramide (Gb3). We produced mutants with alanine substitutions for residues found near the cleft between adjacent subunits. Substitution of alanine for phenylalanine 30 (Phe-30) resulted in a fourfold reduction in B subunit binding affinity for Gb3 and a 10-fold reduction in receptor density in a solid-phase binding assay. The interaction of wild-type and mutant B subunits with Pk trisaccharide in solution was examined by titration microcalorimetry. The carbohydrate binding of the mutant was markedly impaired compared with that of the wild type and was too weak to allow calculation of a binding constant. These results demonstrate that the mutation significantly impaired the carbohydrate-binding function of the B subunit. To ensure that the mutation had not caused a significant change in structure, the mutant B subunit was crystallized and its structure was determined by X-ray diffraction. Difference Fourier analysis showed that its structure was identical to that of the wild type, except for the substitution of alanine for Phe-30. The mutation was also produced in the VT1 operon, and mutant holotoxin was purified to homogeneity. The cytotoxicity of the mutant holotoxin was reduced by a factor of 105 compared to that of the wild type in the Vero cell cytotoxicity assay. The results suggest that the aromatic ring of Phe-30 plays a major role in binding of the B subunit to the Galα1-4Galβ1-4Glc trisaccharide portion of Gb3. Examination of the VT1 B crystal structure suggests two potential carbohydrate-binding sites which lie on either side of Phe-30.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1046/j.1365-2958.1996.427962.x
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  • 6
    Electronic Resource
    Electronic Resource
    Detecting outliers in non-redundant diffraction data (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1759-1764 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Outliers are observations which are very unlikely to be correct, as judged by independent observations or other prior information. Such unexpected observations are treated, effectively, as being more informative about possible models, so they can seriously impede the course of structure determination and refinement. The best way to detect and eliminate outliers is to collect highly redundant data, but it is not always possible to make multiple measurements of every reflection. For non-redundant data, the prior expectation given either by a Wilson distribution of intensities or model-based structure-factor probability distributions can be used to detect outliers. This captures mostly the excessively strong reflections, which dominate the features of electron-density maps or, even more so, Patterson maps. The outlier rejection tests have been implemented in a program, Outliar.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444999008471
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  • 7
    Electronic Resource
    Electronic Resource
    Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 905-921 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A new software suite, called Crystallography & NMR System (CNS), has been developed for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing structure-determination programs the architecture of CNS is highly flexible, allowing for extension to other structure-determination methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic structure-determination language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data structures, such as structure factors, electron-density maps, and atomic properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of macromolecular structure determination by X-ray crystallography and solution NMR.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444998003254
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  • 8
    Electronic Resource
    Electronic Resource
    Incorporation of Prior Phase Information Strengthens Maximum-Likelihood Structure Refinement (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 1285-1294 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The application of a maximum-likelihood analysis to the problem of structure refinement has led to striking improvements over the traditional least-squares methods. Since the method of maximum likelihood allows for a rational incorporation of other sources of information, we have derived a likelihood function that incorporates experimentally determined phase information. In a number of different test cases, this target function performs better than either a least-squares target or a maximum-likelihood function lacking prior phases. Furthermore, this target gives significantly better results compared with other functions incorporating phase information. When combined with a procedure to mask `unexplained' density, the phased likelihood target also makes it possible to refine very incomplete models.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444998004119
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  • 9
    Electronic Resource
    Electronic Resource
    Pushing the boundaries of molecular replacement with maximum likelihood (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1373-1382 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The molecular-replacement method works well with good models and simple unit cells, but often fails with more difficult problems. Experience with likelihood in other areas of crystallography suggests that it would improve performance significantly. For molecular replacement, the form of the required likelihood function depends on whether there is ambiguity in the relative phases of the contributions from symmetry-related molecules (e.g. rotation versus translation searches). Likelihood functions used in structure refinement are appropriate only for translation (or six-dimensional) searches, where the correct translation will place all of the atoms in the model approximately correctly. A new likelihood function that allows for unknown relative phases is suitable for rotation searches. It is shown that correlations between sequence identity and coordinate error can be used to calibrate parameters for model quality in the likelihood functions. Multiple models of a molecule can be combined in a statistically valid way by setting up the joint probability distribution of the true and model structure factors as a multivariate complex normal distribution, from which the conditional distribution of the true structure factor given the models can be derived. Tests in a new molecular-replacement program, Beast, show that the likelihood-based targets are more sensitive and more accurate than previous targets. The new multiple-model likelihood function has a dramatic impact on success.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901012471
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  • 10
    Electronic Resource
    Electronic Resource
    Extending the limits of molecular replacement through combined simulated annealing and maximum-likelihood refinement (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 181-190 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Phases determined by the molecular-replacement method often suffer from model bias. In extreme cases, the refinement of the atomic model can stall at high free R values when the resulting electron-density maps provide little indication of how to correct the model, sometimes rendering even a correct solution unusable. Here, it is shown that several recent advances in refinement methodology allow productive refinement, even in cases where the molecular-replacement-phased electron-density maps do not allow manual rebuilding. In test calculations performed with a series of homologous models of penicillopepsin using either backbone atoms, or backbone atoms plus conserved core residues, model bias is reduced and refinement can proceed efficiently, even if the initial model is far from the correct one. These new methods combine cross-validation, torsion-angle dynamics simulated annealing and maximum-likelihood target functions. It is also shown that the free R value is an excellent indicator of model quality after refinement, potentially discriminating between correct and incorrect molecular-replacement solutions. The use of phase information, even in the form of bimodal single-isomorphous-replacement phase distributions, greatly improves the radius of convergence of refinement and hence the quality of the electron-density maps, further extending the limits of molecular replacement.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444998006635
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