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  • 42.60  (1)
  • Atomic and Molecular Physics  (1)
  • Chemistry and Materials (General)  (1)
  • 2000-2004  (2)
  • 1980-1984  (1)
  • 1935-1939
  • 1
    ISSN: 1432-0649
    Keywords: 42.60 ; 07.65
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Type of Medium: Electronic Resource
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  • 2
    Publication Date: 2019-07-13
    Description: Two of Ernest Overton's lasting contributions to biology are the Meyer-Overton relationship between the potency of an anesthetic and its solubility in oil, and the Overton rule which relates the permeability of a membrane to the oil-water partition coefficient of the permeating molecule. A growing body of experimental evidence, however, cannot be reconciled with these theories. In particular, the molecular nature of membranes, unknown to Overton, needs to be included in any description of these phenomena. Computer simulations are ideally suited for providing atomic-level information about the behavior of small molecules in membranes. The authors discuss simulation studies relevant to Overton's ideas. Through simulations it was found that anesthetics tend to concentrate at interfaces and their anesthetic potency correlates better with solubility at the water-membrane interface than with solubility in oil. Simulation studies of membrane permeation revealed the anisotropic nature of the membranes, as evidenced, for example, by the highly nonuniform distribution of free volume in the bilayer. This, in turn, influences the diffusion rates of solutes, which increase with the depth in the membrane. Small solutes tend to move by hopping between voids in the bilayer, and this hopping motion may be responsible for the deviation from the Overton rule of the permeation rates of these molecules.
    Keywords: Atomic and Molecular Physics
    Type: Science Definition Team Meeting; Jun 02, 2000 - Jun 03, 2000; Monterey, CA; United States
    Format: text
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  • 3
    Publication Date: 2019-07-18
    Description: The main application considered in this paper is predicting true kinases from randomly permuted kinases that share the same length and amino acid distributions as the true kinases. Numerous methods already exist for this classification task, such as HMMs, motif-matchers, and sequence comparison algorithms. We build on some of these efforts by creating a vector from the output of thousands of structurally based HMMs, created offline with Pfam-A seed alignments using SAM-T99, which then must be combined into an overall classification for the protein. Then we use a Support Vector Machine for classifying this large ensemble Pfam-Vector, with a polynomial and chisquared kernel. In particular, the chi-squared kernel SVM performs better than the HMMs and better than the BLAST pairwise comparisons, when predicting true from false kinases in some respects, but no one algorithm is best for all purposes or in all instances so we consider the particular strengths and weaknesses of each.
    Keywords: Chemistry and Materials (General)
    Type: RECOMB 2002: 6th Annual International Conference on Research in Computational Molecular Biology; Apr 18, 2002 - Apr 21, 2002; Washington, DC; United States
    Format: text
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