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  • 1
    Electronic Resource
    Electronic Resource
    Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4 (1996)
    Springer
    Journal of computer aided molecular design 10 (1996), S. 293-304 
    Details
    ISSN: 1573-4951
    Keywords: Inhibitor ; Receptor ; Simulated annealing ; Drug design
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary AutoDock 2.4 predicts the bound conformations of a small, flexible ligand to a nonflexible macromolecular target of known structure. The technique combines simulated annealing for conformation searching with a rapid grid-based method of energy evaluation based on the AMBER force field. AutoDock has been optimized in performance without sacrificing accuracy; it incorporates many enhancements and additions, including an intuitive interface. We have developed a set of tools for launching and analyzing many independent docking jobs in parallel on a heterogeneous network of UNIX-based workstations. This paper describes the current release, and the results of a suite of diverse test systems. We also present the results of a systematic investigation into the effects of varying simulated-annealing parameters on molecular docking. We show that even for ligands with a large number of degrees of freedom, root-mean-square deviations of less than 1 Å from the crystallographic conformation are obtained for the lowest-energy dockings, although fewer dockings find the crystallographic conformation when there are more degrees of freedom.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00124499
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  • 2
    Electronic Resource
    Electronic Resource
    Design of stapled DNA-minor-groove-binding molecules with a mutable atom simulated annealing method (1997)
    Springer
    Journal of computer aided molecular design 11 (1997), S. 539-546 
    Details
    ISSN: 1573-4951
    Keywords: Rational drug design ; DNA-minor-groove-binding molecules
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We report the design of optimal linker geometries for the synthesis of stapledDNA-minor-groove-binding molecules. Netropsin, distamycin, and lexitropsinsbind side-by-side to mixed-sequence DNA and offer an opportunity for thedesign of sequence-reading molecules. Stapled molecules, with two moleculescovalently linked side-by-side, provide entropic gains and restrain theposition of one molecule relative to its neighbor. Using a free-atom simulatedannealing technique combined with a discrete mutable atom definition, optimallengths and atomic composition for covalent linkages are determined, and anovel hydrogen bond ‘zipper’ is proposed to phase two molecules accuratelyside-by-side.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1007985019866
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