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  • Computational Chemistry and Molecular Modeling  (2)
  • Binding sites  (1)
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  • 1
    Electronic Resource
    Electronic Resource
    Determination of clefts in receptor structures (1989)
    Springer
    Journal of computer aided molecular design 3 (1989), S. 133-147 
    Details
    ISSN: 1573-4951
    Keywords: Automatic determination of clefts ; Drug design ; Binding sites ; Dihydrofolate reductase ; Trypsin ; Voronoi tessellation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The automatic determination of atoms which comprise a cleft in a receptor is of great importance in computer-aided drug design. X-ray studies of ligand/receptor pairs show that the ligand is often located in a cleft so that this structural feature will indicate a putative binding site. This information can be used in the design of new drugs by database searching and by automatic structure generation. The methods presented in this paper will find the complete accessible surface in a slice through a receptor and also all the clefts and dimples in this surface, using the properties of the Voronoi tessellation of the receptor. Clefts and binding sites can now be determined quickly and without observer bias.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01557724
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    A ring-bracing approach to computer-assisted ligand design (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 233-240 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Rigid inhibitors suffer a smaller loss of conformational entropy when they bind to a macromolecular receptor than their acyclic counterparts. They can also be useful for elucidating pharmacophores due to their reduced conformational space and may be more amenable to synthesis. Computational approaches to rational drug design should therefore take these factors into consideration when suggesting possible compounds. We describe how an acyclic chain which links two parts of a receptor site can be ‘braced’ using ring templates. The acyclic chains may be produced from a number of sources, including lattices or the structures of known inhibitors. The resulting structures contain a rich variety of isolated and fused ring systems, which provide many useful molecular skeletons for subsequent inhibitor design. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150213
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  • 3
    Electronic Resource
    Electronic Resource
    Determination of molecular topology and atomic hybridization states from heavy atom coordinates (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 891-898 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method is presented for the derivation of hybridization states and connectivity within molecules from the atomic numbers and coordinates of heavy atoms. The algorithm utilizes bond length data from studies of the Cambridge Structural Database (Allen et al., J. Chem. Soc. Perkin Trans. II, S1, (1987)). The program, IDATM, is useful for processing input to hydrogen-adding routines and molecular mechanics programs, as it minimizes the amount of manual preprocessing required. IDATM has been tested on a range of crystallographically determined structures, including poorly determined structures, with a successful assignment of hybridization for over 99% of the atoms in the set.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540120716
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