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  • 1
    Electronic Resource
    Electronic Resource
    Predicting helical segments in proteins by a helix-coil transition theory with parameters derived from a structural database of proteins (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 344-359 
    Details
    ISSN: 0887-3585
    Keywords: helix stabilizing/destabilizing interactions ; helix-capping motifs ; helical boundaries ; structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A novel helix-coil transition theory has been developed. This new theory contains more types of interactions than similar theories developed earlier. The parameters of the models were obtained from a database of 351 nonhomologous proteins. No manual adjustment of the parameters was performed. The interaction parameters obtained in this manner were found to be physically meaningful, consistent with current understanding of helix stabilizing/destabilizing interactions. Novel insights into helix stabilizing/destabilizing interactions have also emerged from this analysis. The theory developed here worked well in sorting out helical residues from amino acid sequences. If the theory was forced to make prediction on every residue of a given amino acid sequence, its performance was the best among ten other secondary structural prediction algorithms in distinguishing helical residues from nonhelical ones. The theory worked even better if one only required it to make prediction on residues that were “predictable” (identifiable by the theory); 〉90% predictive reliability could be achieved. The helical residues or segments identified by the helix-coil transition theory can be used as secondary structural contraints to speed up the prediction of the three-dimensional structure of a protein by reducing the dimension of a computational protein folding problem. Possible further improvements of this helix-coil transition theory are also discussed. Proteins 28:344-359, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
  • 2
    Electronic Resource
    Electronic Resource
    Hydration of superoxide studied by molecular dynamics simulation (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1003-1008 
    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: Molecular dynamics was used to study the hydration of superoxide (O2-). The Helmholtz free energy of hydration of O2- was estimated by the thermodynamic integration method. The diffusion of O2- and the water structure around O2- were also studied. Two water models were used in the calculations and the results were compared to experiments.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110812
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Partial electrostatic charges for the active center of Cu, Zn superoxide dismutase (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 346-350 
    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: Atomic partial charges for three model systems that mimic the metal-ligand moiety of the active site in the enzyme Cu, Zn superoxide dismutase (SOD) have been calculated at the ab initio level. The model systems include copper and zinc complexes with imidazole, formate and ammonia ligands. The partial charges thus obtained have been incorporated into force fields for molecular simulations. Simulations carried out with these force fields justify the need for specialized charge assignments for the metals and their ligands.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110309
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    Paper (German National Licenses)
    Fulltext
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