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  • Contact potentials  (1)
  • Receptor mapping  (1)
  • combinatorial chemistry  (1)
  • 1
    Electronic Resource
    Electronic Resource
    The measurement of molecular diversity by receptor site interaction simulation (1998)
    Springer
    Journal of computer aided molecular design 12 (1998), S. 441-449 
    Details
    ISSN: 1573-4951
    Keywords: chemical leads ; combinatorial chemistry ; compound libraries ; drug discovery ; receptor targets ; similarity measures
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The assembly of large compound libraries for the purpose of screening against various receptor targets to identify chemical leads for drug discovery programs has created a need for methods to measure the molecular diversity of such libraries. The method described here, for which we propose the acronym RESIS (for Receptor Site Interaction Simulation), relates directly to this use. A database is built of three-dimensional representations of the compounds in the library and a set of three-point three-dimensional theoretical receptor sites is generated based on putative hydrophobic and polar interactions. A series of flexible, three-dimensional searches is then performed over the database, using each of the theoretical sites as the basis for one such search. The resulting pattern of hits across the grid of theoretical receptor sites provides a measure of the molecular diversity of the compound library. This can be conveniently displayed as a density map which provides a readily comprehensible visual impression of the library diversity characteristics. A library of 7500 drug compounds derived from the CIPSLINEPC databases was characterized with respect to molecular diversity using the RESIS method. Some specific uses for the information obtained from application of the method are discussed. A comparison was made of the results from the RESIS method with those from a recently published two-dimensional approach for assessing molecular diversity using sets of compounds from the Maybridge database (MAY).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008023429373
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Objective models for steroid binding sites of human globulins (1997)
    Springer
    Journal of computer aided molecular design 11 (1997), S. 93-110 
    Details
    ISSN: 1573-4951
    Keywords: QSAR ; Voronoi ; Receptor mapping ; Steroids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We report the application of a recently developed alignment-free 3D QSAR method [Crippen,G.M., J. Comput. Chem., 16 (1995) 486] to a benchmark-type problem. The test systeminvolves the binding of 31 steroid compounds to two kinds of human carrier protein. Themethod used not only allows for arbitrary binding modes, but also avoids the problems oftraditional least-squares techniques with regard to the implicit neglect of informative outlyingdata points. It is seen that models of considerable predictive power can be obtained even witha very vague binding site description. Underlining a systematic, but usually ignored, problemof the QSAR approach, there is not one unique type of model but, rather, an entire manifoldof distinctly different models that are all compatible with the experimental information. Fora given model, there is also a considerable variation in the found binding modes, illustratingthe problems that are inherent in the need for ’correct‘ molecular alignment in conventional3D QSAR methods.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008031629127
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Failures of inverse folding and threading with gapped alignment (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 167-171 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; Lattice models ; Contact potentials ; Protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To calculate the tertiary structure of a protein from its amino acid sequence, the thermodynamic approach requires a potential function of sequence and conformation that has its global minimum at the native conformation for many different proteins. Here we study the behavior of such functions for the simplest model system that still has some of the features of the protein folding problem, namely two-dimensional square lattice chain configurations involving two residue types. First we show that even the given contact potential, which by definition is used to identify the folding sequences and their unique native conformations, cannot always correctly select which sequences will fold to a given structure. Second, we demonstrate that the given contact potential is not always able to favor the native alignment of a native sequence on its own native conformation over other gapped alignments of different folding sequences onto that same conformation. Because of these shortcomings, even in this simple model system in which all conformations and all native sequences are known and determined directly by the given potential, we must reexamine our expectations for empirical potentials used for inverse folding and gapped alignment on more realistic representations of proteins. © 1996 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
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