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  • 1
    Electronic Resource
    Electronic Resource
    Conformationally restricted analogs of disoxaril: a comparison of the activity against human rhinovirus type 14 and 1A (1992)
    s.l. : American Chemical Society
    Journal of medicinal chemistry 35 (1992), S. 4690-4695 
    Details
    ISSN: 1520-4804
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/jm00103a006
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  • 2
    Electronic Resource
    Electronic Resource
    Interferometry with Atoms and Molecules (1995)
    Oxford, UK : Blackwell Publishing Ltd
    Annals of the New York Academy of Sciences 755 (1995), S. 0 
    Details
    ISSN: 1749-6632
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Natural Sciences in General
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1749-6632.1995.tb38967.x
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  • 3
    Electronic Resource
    Electronic Resource
    Improved free R factors for cross-validation of macromolecular structure – importance for real-space refinement (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 219-224 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Improvements in free R cross-validation are based on changed scaling procedures and the use, in map calculation, of estimates of the validation amplitudes which are independent of the actual observed values. The deleterious effects of the omitted test data are mitigated by reduction of the test-set size, which is made possible by constraining test and working sets to share the same scaling coefficients, thereby reducing the degrees of freedom and the dependence of free R on data selection. Further improvements come with use of a modified free R factor, R^{\rm free}_{T_{A}}. Instead of omitting the validation reflections from map calculation, their amplitudes are replaced by the average of resolution peers that is (nearly) independent of the actual cross-validation amplitudes. The improvements are relevant to model building, phase refinement by density modification and especially to real-space refinement. Although for real data at about 3 Å resolution, free R factors of about 0.25 are affected little, the precision of the structure is improved by about 0.1 Å. Tests with simulated data show that with good agreement between observed and calculated amplitudes (as in very high resolution studies or simulated refinement tests), free R factors can be improved by factors greater than two.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444998007331
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  • 4
    Electronic Resource
    Electronic Resource
    Real-space molecular-dynamics structure refinement (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 464-468 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Real-space targets and molecular-dynamics search protocols have been combined to improve the convergence of macromolecular atomic refinement. This was accomplished by providing a local real-space target function for the molecular-dynamics program X-PLOR. With poor isomorphous replacement experimental phases, molecular dynamics does not improve real-space refinement. However, with high-quality anomalous diffraction phases convergence is improved at the start of refinement, and torsion-angle real-space molecular dynamics performs better than other available least-squares or maximum-likelihood methods in real or reciprocal space. It is shown that the improvements result from an optimization method that can escape local minima and from a reduction of overfitting through the implicit use of phases and through use of a local refinement in which errors in remote parts of the structure cannot be mutually compensating.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744499801097X
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  • 5
    Electronic Resource
    Electronic Resource
    Determination of the Relative Precision of Atoms in a Macromolecular Structure (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 391-399 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Several real-space indices and temperature factors are compared with respect to their correlation with atomic positional error and their ability to indicate atoms and residues with the worst of subtle errors. The best index, rED, is a correlation coefficient between model and map electron densities, similar to one proposed earlier, but incorporating two improvements. Firstly, resolution is accounted for explicitly by calculating the model electron density by Fourier transformation of resolution-truncated scattering factors. Secondly, the deviation between model and map electron densities is assigned to neighboring atoms according to their contribution to the electron density of each grid point. With maps of various qualities, rED is the single index with best correlation to atomic error with grouped or individual atoms, and it is the most reliable indicator of poor residues. With poorer omit maps, imprecision of individual atoms is best diagnosed by a combination of low rED or high B factor. With the improved methods, 60–70% of the least precise atoms can detected in a fully refined structure. Similarly, 40–80% of the least precise atoms of an unrefined model can be detected by comparison with an isomorphous replacement map. This is useful in assessing and improving the quality of a model, but not sufficient to confidently validate all atoms of a structure at sub-atomic resolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444997011530
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  • 6
    Electronic Resource
    Electronic Resource
    Critical initial real-space refinement in the structure determination of arginine kinase (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 835-845 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Arginine kinase (AK), a homologue of creatine kinase, catalyses the reversible transfer of a phosphoryl group between a guanidino phosphate and ADP. The family of phosphagen kinases eluded structure determination for over 25 years until an inactive form creatine kinase (CK) structure was determined [Fritz-Wolf et al. (1996). Nature (London), 381, 341–345]. The structure determination of the active-form transition-state complex was non-trivial, owing to the distant relatedness and domain reorientation of AK compared with CK. Phases from a molecular-replacement solution of the large domain, supplemented by single isomorphous replacement and inter-crystal averaging, did not reveal interpretable electron density for the small domain. Reciprocal-space refinement of the initial model (Rfree = 0.54) by any of the commonly used methods, including post facto application of maximum-likelihood methods, led to overfitting without significant improvement of the partial initial model. By contrast, in the local real-space refinements which proved successful, the interdependence of atoms is limited to immediate neighbors, and atomic positions are not influenced by errors or omissions in remote parts of the structure. Modest improvement was possible without overfitting, and this was critical to the calculation of improved phases. Phases were refined and extended from 4.0 to 2.5 Å resolution by Fourier inversion of omit maps, combination with isomorphous replacement phases and averaging between crystal forms, after several batches of real- and reciprocal-space atomic refinement. The final structure refinement, against a 1.86 Å cryo data set yielded a high-quality model with R = 0.196 and Rfree = 0.224.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444999000888
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  • 7
    Electronic Resource
    Electronic Resource
    Sliding-layer conformational change limited by the quaternary structure of plant RuBisCO (1987)
    [s.l.] : Nature Publishing Group
    Nature 329 (1987), S. 354-356 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The importance of RuBisCO is not only that it is the source of all food through its catalysis of the initial step of the Calvin cycle of photosynthesis, but also that it is a tempting target for protein engineering because it also catalyses the first step in the competing pathway of ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/329354a0
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  • 8
    Electronic Resource
    Electronic Resource
    Modelling of the human intercellular adhesion molecule-1, the human rhinovirus major group receptor (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 227-233 
    Details
    ISSN: 0887-3585
    Keywords: rhinovirus receptor ; ICAM-1 ; structure prediction ; immunoglobulin superfamily ; docking receptor to virus ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model has been built of the amino-terminal domain of the intercellular adhesion molecule-1 (ICAM-1), the receptor for most human rhinovirus serotypes. The model was based on sequence and presumed structural homology to immunoglobulin constant domains. It fits well into the putative receptors attachment site, the canyon, on the human rhinovirus-14 (HRV14) surface in a manner consistent with most of the mutational data for ICMA-1 (Staunton, D. E., Dustin, M. L., Erickson, H. P., Springer, T. A. Cell, in press, 1989) and HRV14 (Colonno, R. J., Condra, J. H., Mizutani, S., Callahan, P. L., Davies, M. E., Murcko, M. A. Proc. Natl. Acad. Sci. U.S.A. 85: 5449-5453, 1988).
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070304
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