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  • Biochemistry  (1)
  • Proteins -- Structure.  (1)
  • Radial distribution function  (1)
  • 1
    Online Resource
    Online Resource
    Newark :John Wiley & Sons, Incorporated,
    Keywords: Proteins -- Structure. ; Electronic books.
    Type of Medium: Online Resource
    Pages: 1 online resource (278 pages)
    Edition: 1st ed.
    ISBN: 9780470141816
    Series Statement: Advances in Chemical Physics Series ; v.148
    DDC: 539 s
    Language: English
    Note: PROTEINS: A THEORETICAL PERSPECTIVE OF DYNAMICS, STRUCTURE, AND THERMODYNAMICS -- CONTENTS -- I. INTRODUCTION -- II. PROTEIN STRUCTURE AND DYNAMICS-AN OVERVIEW -- III. POTENTIAL FUNCTIONS -- IV. DYNAMICAL SIMULATION METHODS -- V. THERMODYNAMIC METHODS -- VI. ATOM AND SIDECHAIN MOTIONS -- VII. RIGID-BODY MOTIONS -- VIII. LARGER-SCALE MOTIONS -- IX. SOLVENT INFLUENCE ON PROTEIN DYNAMICS -- X. THERMODYNAMIC ASPECTS -- XI. EXPERIMENTAL COMPARISONS AND ANALYSIS -- XII. CONCLUDING DISCUSSION -- REFERENCES -- INDEX.
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical chemistry accounts 96 (1997), S. 61-70 
    ISSN: 1432-2234
    Keywords: Key words:Fluids ; Integral equation methods ; Radial distribution function
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. The first two orders of bridge diagrams, those with two and three field points, have been calculated exactly for the Lennard-Jones fluid for several isotherms. The method of calculation was one of expansion in Legendre polynomials, and the dependence of the method on the number of polynomials needed for accurate results was investigated. Thermodynamic and structural properties of the Lennard-Jones fluid calculated from integral equation methods with the inclusion of bridge diagrams were found to be systematically improved. Two attempts at predicting the missing bridge diagrams of even higher order were discussed. The first, which uses the functional form of those diagrams that were calculated exactly, showed no significant improvement. The second, a series sum based on the first two orders of calculated diagrams and motivated by the success of a similar heuristic sum in the case of hard spheres, was extremely successful. When the series sum was employed, thermodynamic and structural quantities were improved to the point where the difference between simulation results and integral equation results was of the same order as the error in the simulations themselves.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 627-634 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present two techniques for implementing a new method of simulating an entire virion. Earlier computer simulations of a capsid protein revealed large edge effects due to the use of free standing boundaries. Because of the size of a given protomer, conventional three-dimensional periodic boundary conditions would be extremely wasteful. This would require an extremely large number of solvent molecules, and therefore would be computationally feasible for only a fragment of the entire virion. The new method employs non-space-filling computational cells in molecular modeling and molecular dynamics with the boundary conditions based on the icosahedral group. The method is general and could be used for any molecular system with a point group symmetry. With this method, the dynamical and spatial intra and interprotomer correlations can be studied at atomic levels. The technique is applicable to any virion with icosahedral symmetry. A sample calculation involving a geometry optimization of the human rhinovirus coat proteins is given to demonstrate the technique.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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