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  • 1
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Biochemistry 27 (1988), S. 5389-5395 
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Biochemistry 21 (1982), S. 2259-2274 
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Macromolecules 15 (1982), S. 1528-1544 
    ISSN: 1520-5835
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 115 (1993), S. 4764-4768 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 6692-6699 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Path integral molecular dynamics (PIMD) simulations of the extended simple point charge (SPC/E) model of liquid water (both H2O and D2O) have been performed in order to find the temperature at which the maximum liquid density is obtained. For comparison, purely classical SPC and SPC/E water have also been simulated over long periods (more than 200 ps). Structural properties and various temperature dependent quantities are reported. Special attention has been given to the fluctuations of pressure and volume in simulations run in the canonical (constant NVT) and isothermal–isobaric (constant NPT) ensembles, respectively. Although a density maximum is detected by monitoring energy–volume correlations as a function of temperature, the large statistical uncertainty in the correlations reduces the significance of this finding. The main conclusions of this work are threefold. First, the use of the energy–volume correlation moment to determine the density maximum appears to be a useful method, although a number of very long simulations of between 0.5–1.0 ns over a fairly wide temperature range are necessary to obtain accurate results. Second, neither the SPC nor the SPC/E water models are able to reproduce the density of cold water accurately. Finally, a quantum mechanical treatment of the water model is necessary to correctly represent the structure, energy, and fluctuations of the condensed phase.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 96 (1992), S. 4699-4704 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The transport of small molecules through a polymer membrane is modeled using the computer simulation technique of molecular dynamics (MD). The transport coefficient is derived from a combination of the excess free energy and the diffusion constant. Both properties are derived from MD simulations, applied to helium and methane in polydimethylsiloxane (PDMS). The diffusional process appears to have the character of a jump diffusion for methane and less so for helium. Jumps are allowed by fluctuations of the size and shape of holes. Experimental diffusion constants are well reproduced. The excess free energies, determined by a particle insertion method, are lower by 5–7 kJ/mol than experimental values. It is shown that, as a result of a higher solubility, methane has a higher permeability constant than helium, despite its lower diffusion constant.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 22 (1989), S. 1-8 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The method of crystallographic refinement using molecular dynamics [Brünger, Kuriyan & Karplus (1987). Science, 235, 458–460] has been implemented to work with the GROMOS simulation package. It has been tested by applying it to the structure of phospholipase A2. The structure of this molecule had previously been refined at high resolution with conventional methods. The new method successfully refined the initial multi-isomorphous replacement structure, removing most of the errors, without any manual intervention. All the refinement was performed at 300 K. The use of lower-resolution data allows greater conformational transitions to occur whereas the inclusion of high-resolution data results in a more accurate structure.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature 293 (1981), S. 677-678 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The protein used, bovine pancreatic trysin inhibitor (PTI), consists of 454 heavy atoms. (In the calculations, the hydrogen atoms were incorporated in the heavy atoms to which they are bound.) There are also four internally hydrogen-bonded water molecules. The empirical potential function (see refs ...
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 0887-3585
    Keywords: distance-restrained molecular dynamics ; 2D NOE-spectroscopy ; tertiary structure ; solution conformations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The technique of two-dimensional nuclear magnetic resonance (2D-NMR) has recently assumed an active role in obtaining information on structures of polypeptides, small proteins, sugars, and DNA fragments in solution. In order to generate spatial structures from the atom-atom distance information obtained by the NMR method, different procedures have been developed. Here we introduce a combined procedure of distance geometry (DG) and molecular dynamics (MD) calculations for generating 3D structures that are consistent with the NMR data set and have reasonable internal energies. We report the application of the combined procedure on the lac repressor DNA binding domain (headpiece) using a set of 169 NOE and 17 “hydrogen bond” distance constraints. Eight of ten structures generated by the distance geometry algorithm were refined within 10 ps MD simulation time to structures with low internal energies that satisfied the distance constraints.Although the combination of DG and MD was designed to combine the good sampling properties of the DG algorithm with an efficient method of lowering the internal energy of the molecule, we found that the MD algorithm contributes significantly to the sampling as well.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989), S. 104-127 
    ISSN: 0887-3585
    Keywords: lac repressor; lac operator ; lac headpiece-operator complex ; protein-DNA specificity ; molecular dynamics ; computer simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The results of a 125 psec molecular dynamics simulation of a lac headpiece-operator complex in aqueous solution are reported. The complexsatisfies essentially all experimental distance information derived from two-dimensional nuclear magnetic resonance (2-D-NMR) studies. The interaction between lac repressor headpiece and its operator based on many direct- and water-mediated hydrogenbonds and nonpolar contacts which allow the formation of a tight complex. Nostable hydrogen bonds between side chains and bases and found, while specific contacts occur between both nonpolar groups and, to a lesserextent, through water-mediated hydrogen bonds. The simulated complex structure in water is intrinsically stable without application of nuclear Overhauser effect (NOE) distance restraints, while being compatible with most of the available biochemical, genetic, andchemically induced dynamic nuclear polarization (CIDNP) data.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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