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  • 1
    Electronic Resource
    Electronic Resource
    Conformational energy downward driver (CEDD): Characterization and calibration of the method (1995)
    Springer
    Journal of computer aided molecular design 9 (1995), S. 55-64 
    Details
    ISSN: 1573-4951
    Keywords: Torsional driver ; Rotatable bonds ; Optimization ; Conformational analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A method has been developed that allows one to drive a molecule to conformations of lowest energy given the starting conformation, the identity of the rotatable bonds and the step size. This method has proved useful in our hands in the drug design arena where it is frequently more important to get ‘low-energy’ conformers of a molecule that match some other (e.g. pharmacophoric or enzyme pocket) requirements than to exhaustively enumerate all possible low-energy conformations for each of the molecules to be studied. The method has been shown to work in the test cases studied to date. Furthermore, so far it has been shown to be sufficiently fast to be used for molecules containing up to 70 rotatable bonds.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00117278
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Docking flexible molecules: A case study of three proteins (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 1405-1419 
    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 genetic algorithm (GA) conformation search method is used to dock a series of flexible molecules into one of three proteins. The proteins examined are thermolysin (tmn), carboxypeptidase A (cpa), and dihydrofolate reductase (dfr). In the latter two proteins, the crystal ligand was redocked. For thermolysin, we docked eight ligands into a protein conformation derived from a single crystal structure. The bound conformations of the other ligands in tmn are known. In the cpa and dfr cases, and in seven of the eight tmn ligands, the GA docking method found conformations within 1.6 Å root mean square (rms) of the relaxed crystal conformation. © 1995 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540161109
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    A comparison of a direct search method and a genetic algorithm for conformational searching (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1142-1151 
    Details
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present results from the application of two conformational searching methods: genetic algorithms (GA) and direct search methods for finding low energy conformations of organic molecules. GAs are in a class of biologically motivated optimization methods that evolve a population of individuals in which individuals who are more “fit” have a higher probability of surviving into subsequent generations. The parallel direct search method (PDS) is a type of pattern search method that uses an adaptive grid to search for minima. Both methods found energies equal to or lower than the energy of the relaxed crystal structure in all cases, at a relatively small cost in CPU time. We suggest that either method would be a good candidate to find 3-D conformations in a large scale screening application. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
  • 4
    Electronic Resource
    Electronic Resource
    Conformational searching methods for small molecules. III. Study of stochastic methods available in SYBYL and MACROMODEL (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1171-1182 
    Details
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In a continuing effort to provide the computational community with a reference work comparing all of the available conformer searching methods, we have exposed the standard set of small molecules to two commonly used stochastic searching techniques. Advantages and limitations of these methods are discussed. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
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