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  • 1
    Electronic Resource
    Electronic Resource
    Prediction of Protein Binding to DNA in the Presence of Water-Mediated Hydrogen Bonds (1999)
    Springer
    Journal of molecular modeling 5 (1999), S. 125-133 
    Details
    ISSN: 0948-5023
    Keywords: Keywords  Hydrogen Bonds ; Protein-DNA Binding ; Specificity ; Water
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We extend our previous analysis of binding specificity of DNA-protein complexes to complexes containing water-mediated bridges. Inclusion of water bridges between phosphate and base, phosphate and sugar, as well as proteins and DNA, improves the prediction of specificity; six data sets studied in this paper yield correct predictions for all base pairs that have two or more hydrogen-bonds. Beside massive computation, our approach relies highly on experimental data. After deriving protein structures from DNA-protein complexes in which coordinates were established by X-ray diffraction techniques, we analysed all possible DNA sequences to which these proteins might bind, ranking them in terms of Lennard-Jones potential for the optimal docking configuration. Our prediction algorithm rests on the following assumptions: (1) specificity comes mainly from direct hydrogen bonding; (2) electrostatic forces stabilise DNA-protein complexes and contribute only weakly to specificity since they occur at the charged phosphate groups; (3) Van der Waals forces and electrostatic interactions between positively charged groups on the protein and phosphates on DNA can be neglected as they contribute primarily to the free energy of stabilisation as opposed to specificity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s008940050121
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  • 2
    Electronic Resource
    Electronic Resource
    Polymer-protected cu/pd bimetallic clusters (1994)
    Weinheim : Wiley-Blackwell
    Advanced Materials 6 (1994), S. 245-247 
    Details
    ISSN: 0935-9648
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/adma.19940060316
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Preparation of polymer-protected Pt/Co bimetallic colloid and its catalytic properties in selective hydrogenation of cinnamaldehyde to cinnamyl alcohol (1996)
    New York, NY : Wiley-Blackwell
    Polymers for Advanced Technologies 7 (1996), S. 719-722 
    Details
    ISSN: 1042-7147
    Keywords: Pt/Co bimetallic colloid ; selective hydrogenation ; cinnamaldehyde ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A polymer-protected Pt/Co bimetallic colloid with a molar ratio of 3:1 has been prepared by a polyol process. Over the above Pt/Co bimetallic colloid catalyst, cinnamaldehyde can be selectively hydrogenated to cinnamyl alcohol with 99.8% selectivity at 96.2% conversion.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
  • 4
    Electronic Resource
    Electronic Resource
    Immobilization of polymer-protected metal colloid catalysts by the formation of polymer hydrogen bond complexes (1996)
    New York, NY : Wiley-Blackwell
    Polymers for Advanced Technologies 7 (1996), S. 634-638 
    Details
    ISSN: 1042-7147
    Keywords: polymer-protected metal colloid ; immobilization ; catalyst ; hydrogenation ; cyclopentadiene ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: poly(N-vinyl-2-pyrrolidone)-(PVP) and polyvinyl alcohol-(PVA) protected nanoscopic noble metal colloidal catalysts were immobilized to prepare the corresponding heterogeneous catalysts by forming polymer hydrogen bond complexes of polyacrylic acid (PAA) with PVP or PVA. A PVP-PAA-Pd catalyst was found to be very active and selective for the partial hydrogenation of cyclopentadiene to cyclopentene.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
  • 5
    Electronic Resource
    Electronic Resource
    Analysis and prediction of hydrogen bonding in protein-DNA complexes using parallel processors (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1712-1725 
    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: A number of essential biological functions are controlled by proteins that bind to specific sequences in genomic DNA. In this article we present a simplified model for analyzing DNA-protein interactions mediated exclusively by hydrogen bonds. Based on this model, an optimized algorithm for geometric pattern recognition was developed. The large number of local energy minima are efficiently screened by using a geometric approach to pattern matching based on a square-well potential. The second part of the algorithm represents a closed form solution for minimization based on a quadratic potential. A Monte Carlo method applied to a modified Lennard-Jones potential is used as a third step to rank DNA sequences in terms of pattern matching. Using protein structures derived from four DNA-protein complexes with three-dimensional coordinates established by X-ray diffraction analysis, all possible DNA sequences to which these proteins could bind were ranked in terms of binding energies. The algorithm predicts the correct DNA sequence when at least two hydrogen bonds per base pair are involved in binding to the protein, providing a partial solution to the three-dimensional docking problem. This study lays a framework for future refinements of the algorithm in which the number of assumptions made in the present analysis are reduced. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.3
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    Paper (German National Licenses)
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