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  • Chemistry  (2)
  • Molecular shape  (1)
  • 1990-1994  (2)
  • 1965-1969  (1)
  • 1
    Electronic Resource
    Electronic Resource
    A shape- and chemistry-based docking method and its use in the design of HIV-1 protease inhibitors (1994)
    Springer
    Journal of computer aided molecular design 8 (1994), S. 231-242 
    Details
    ISSN: 1573-4951
    Keywords: Ligand design ; Molecular shape ; DOCK ; Database searching
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The program DOCK [1,2] has been used successfully to identify molecules which will bind to a specified receptor [3]. The original method ranks molecules based on their shape complementarity to the receptor site and relies on the chemist to bring the appropriate electrostatic or hydrogen bond properties into the molecular skeletons obtained in the search. This is useful when screening a small database of compounds, where it is not likely that molecules with both the correct shape and electrostatic properties will be found. As large databases are more likely to have redundant molecular shapes with a variety of functionality (e.g., members of a congeneric series), it would be useful to have a method which identifies molecules with both the correct shape and functionality. To this end we have modified the DOCK 1.0 method to target user-specified atom types to selected positions in the receptor site. The target sites can be chosen based on structural evidence, calculation or inspection. Targeted-DOCK improves the ability of the DOCK method to find the crystallographically determined binding mode of a ligand. Additionally, targeted-DOCK searches a database of small molecules at 100–1000 times the rate of DOCK 1.0, allowing more molecules to be screened and more sophisticated scoring schemes to be employed. Targeted-DOCK has been used successfully in the design of a novel non-peptide inhibitor of HIV-1 protease.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00126742
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  • 2
    Electronic Resource
    Electronic Resource
    The motion of algae in turbulent flow (1965)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 7 (1965), S. 295-308 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Large cultures of microscopic, unicellular algae have been proposed as a means of maintaining a life-supporting atmosphere in a closed, manned system. To achieve vigorous growth of the algal culture it is necessary to subject individual algae alternately to short periods of high intensity light and darkness. One of the means suggested for obtaining a favorable light-dark sequence for photosynthesis is to cause turbulence in a closed channel on which light is incident. Since light is rapidly attenuated in a dense suspension, there will be illuminated regions adjacent to the channel walls and a dark central core. The random motions of turbulence normal to the direction of flow would move the algae alternately from the illuminated regions to the dark region and back again. This paper indicates a method for analyzing the motion of algae into and out of the illuminated region of a channel formed by flat, parallel, transparent plates, with light incident on the plates. Matching of a probability model with a diffusion model makes it possible to estimate the light-dark sequence which could be achieved by turbulence. The results indicate that favorable sequences by this mechanism are unlikely.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260070209
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  • 3
    Electronic Resource
    Electronic Resource
    Application of the distance geometry algorithm to cyclic oligopeptide conformation searches (1990)
    New York : Wiley-Blackwell
    Biopolymers 30 (1990), S. 45-56 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distance geometry algorithm as embodied in the program DGEOM was examined as a method for searching cyclic peptide conformations. Conformations were randomly generated using covalent distance and chirality constraints, but torsion angle rather than distance sampling was used for 1, 4 relationships. Structures so generated were energy minimized by a fixed number of iterations using the molecular mechanics program AMBER 3.0; electrostatic terms were excluded in the minimization. The effectiveness of this procedure in sampling conformational space for cyclic peptides was measured by the ability to recover, from a set of 500 structures, conformations similar to those experimentally observed for six cyclic peptides containing from 8 to 20 rotatable backbone bonds. Structures similar to experimental structures were recovered in a 16-bond case, but not for a 20-bond example. The method was also applied, with constraints on the peptide bond angles ω, to an additional example containing 21 ring bonds.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360300107
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