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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Journal of computer aided molecular design 9 (1995), S. 373-379 
    ISSN: 1573-4951
    Keywords: Geometric keys ; Molecular descriptors ; Database sereening ; Database clustering ; Pharmacophores
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Distances between key functional groups have been used for some time as molecular descriptors in 3D database screening and clustering calculations. More recently, a number of groups have explored triplets of molecular centers to describe key ligand features in terms of the properties of triangles. Three-body distances are attractive, since they retain more information than pairwise representations. In most applications, the triangular descriptors have been used to detail molecular shape, using all the constituent atoms or molecular surface points as descriptor centers. As a consequence, the database keying times were such that only single conformers could be considered during molecular descriptor calculations. In this paper we reduce the points used in the molecular description down to the key functional centers, as applied in 3D pharmacophore database searches. Molecular triplets can then be calculated which describe the relative dispositions of differing functional groups, made up from multiple molecular conformations of a given molecule. The new triplet descriptors are compared with classical pairwise distance measures using a variety of pharmacophores, and their potential in database screening, clustering and pharmacophore identification is discussed.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Journal of computer aided molecular design 8 (1994), S. 299-306 
    ISSN: 1573-4951
    Keywords: Molecular recognition ; Ligand binding ; Complementarity ; Hydropathy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Methods that predict geometries of ligands binding to receptor molecules can facilitate ligand discovery and yield information on the factors governing complementarity. Here, the use of atomic hydrophobicities in evaluating binding modes has been examined with four ligand-receptor complexes of known structure. In each system, hundreds of hypothetical binding orientations were generated with DOCK and evaluated using the HINT (Hydropathic INTeractions) exponential function and atomic hydrophobic constants. In three of the four systems, the experimental binding mode received the best HINT score; in the fourth system, the experimental binding mode scored only slightly lower than a similar, apparently reasonable orientation. The HINT function may be generally useful as a scoring method in molecular docking.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Journal of computer aided molecular design 6 (1992), S. 607-628 
    ISSN: 1573-4951
    Keywords: Molecular similarity ; Database clustering ; Molecular comparison
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A new formalism for molecular shape description is described. The formalism, based on considering each molecule as a collection of its 3-atom submolecules, is applied to both the graph theory and geometrical coordinate representations of molecules. The timing results for shape description of several databases indicate that this new method is applicable to large databases. Furthermore, results from clustering a small database show good agreement with clustering results obtained by a distance-matching algorithm.
    Type of Medium: Electronic Resource
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