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  • 1
    Electronic Resource
    Electronic Resource
    Experimentally verifying molecular dynamics simulations through fluorescence anisotropy measurements (1991)
    s.l. : American Chemical Society
    Biochemistry 30 (1991), S. 1173-1179 
    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/bi00219a002
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Fluorescence analysis of calmodulin mutants containing tryptophan: conformational changes induced by calmodulin-binding peptides from myosin light chain kinase and protein kinase II (1991)
    s.l. : American Chemical Society
    Biochemistry 30 (1991), S. 7615-7630 
    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/bi00244a034
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    THE STRUCTURAL BIOLOGY OF MOLECULAR RECOGNITION BY VANCOMYCIN (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 29 (2000), S. 265-289 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Vancomycin is the archetype among naturally occurring compounds known as glycopeptide antibiotics. Because it is a vital therapeutic agent used worldwide for the treatment of infections with gram-positive bacteria, emerging bacterial resistance to vancomycin is a major public health threat. Recent investigations into the mechanisms of action of glycopeptide antibiotics are driven by a need to understand their detailed mechanism of action so that new agents can be developed to overcome resistance. These investigations have revealed that glycopeptide antibiotics exhibit a rich array of complex cooperative phenomena when they bind target ligands, making them valuable model systems for the study of molecular recognition.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.29.1.265
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    Paper (German National Licenses)
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  • 4
    Electronic Resource
    Electronic Resource
    Buried water in homologous serine proteases (1992)
    s.l. : American Chemical Society
    Biochemistry 31 (1992), S. 12785-12791 
    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/bi00166a011
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    Paper (German National Licenses)
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  • 5
    Electronic Resource
    Electronic Resource
    Simulated dipeptide recognition by vancomycin (1997)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 10 (1997), S. 73-87 
    Details
    ISSN: 0952-3499
    Keywords: glycopeptide antibiotics ; free energy perturbation ; molecular dynamics simulation ; molecular recognition ; computer-assisted drug design ; 2D NMR ; simulated annealing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The antimicrobial activity of vancomycin and related glycopeptide antibiotics is due to stereospecific recognition of polypeptide components in bacterial cell walls. To better understand how these antibiotics recognize polypeptide determinants, we have developed dynamic models of the complexes formed by the vancomycin aglycon and two different dipeptide ligands, Ac-D-ala-D-ala and Ac-D-ala-gly. Molecular dynamics simulations of the two complexes, initially conditioned with distance constraints derived from two-dimensional nuclear magnetic resonance (NMR) studies, are conformationally stable and propagate in a manner consistent with the NMR-derived constraints after the constraints are removed. Free energy calculations accurately predict the relative binding affinity of these two complexes and help validate the simulation models for detailed structural analysis. Although the two ligands adopt similar conformations when bound to the antibiotic, there are clear differences in the configuration of intermolecular hydrogen bonds, the overall shape of the antibiotic, and other structural features of the two complexes. This analysis illustrates how complex structural and dynamic factors interrelate and contribute to differences in binding affinity. © 1997 John Wiley & Sons, Ltd.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
  • 6
    Electronic Resource
    Electronic Resource
    Improved convergence in dual-topology free energy calculations through use of harmonic restraints (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1278-1283 
    Details
    ISSN: 0192-8651
    Keywords: SHAKE ; CHARMM ; molecular mechanics ; free energy perturbation ; molecular dynamics simulation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: When calculating free energy differences between two molecular systems by means of molecular dynamics simulation, accessory potential functions can help eliminate uninteresting configurational entropy contributions, improve convergence, and facilitate reversibility. In this work, we demonstrate that the use of a harmonic potential function to restrain key portions of a molecular system in a free energy perturbation dual-topology molecular dynamics approach dramatically improves convergence and precision of the calculation. Limitations of this technique are illustrated, and its use in conjunction with a fixed bond-length constraint is developed.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1278-1283, 1998
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
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