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  • 1995-1999  (2)
  • Coupling constants  (1)
  • automated assignment  (1)
  • 1
    ISSN: 1573-5001
    Keywords: automated assignment ; combinatorial minimization ; proteins ; threshold accepting
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract The sequential assignment of backbone resonances is the first step in the structure determination of proteins by heteronuclear NMR. For larger proteins, an assignment strategy based on proton side-chain information is no longer suitable for the use in an automated procedure. Our program PASTA (Protein ASsignment by Threshold Accepting) is therefore designed to partially or fully automate the sequential assignment of proteins, based on the analysis of NMR backbone resonances plus Cβ information. In order to overcome the problems caused by peak overlap and missing signals in an automated assignment process, PASTA uses threshold accepting, a combinatorial optimization strategy, which is superior to simulated annealing due to generally faster convergence and better solutions. The reliability of this algorithm is shown by reproducing the complete sequential backbone assignment of several proteins from published NMR data. The robustness of the algorithm against misassigned signals, noise, spectral overlap and missing peaks is shown by repeating the assignment with reduced sequential information and increased chemical shift tolerances. The performance of the program on real data is finally demonstrated with automatically picked peak lists of human nonpancreatic synovial phospholipase A2, a protein with 124 residues.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Angewandte Chemie International Edition in English 34 (1995), S. 1671-1695 
    ISSN: 0570-0833
    Keywords: NMR spectroscopy ; structure elucidation ; Coupling constants ; NMR spectroscopy ; Structure elucidation ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Since their discovery in the early fifties, scalar/coupling constants have been of great interest to the NMR spectroscopist. Their impact on structure determination by NMR spectroscopy is founded on the fact that the size of the coupling constant is directly related to molecular conformation. Today, for most chemical substances the parameters for the Karplus relationship, which relates the vicinial (3-bond) coupling constant to the dihedral angle, have been determined. In addition to proton-proton distances, the application of coupling constants in modern conformational analysis is indispensable. In the study of larger molecules which are of current interest, more and more involved experiments are necessary in order to overcome signal overlap and increasing line widths. A large number of experimental techniques for the determination of coupling constants has been developed; however, for this reason the choice of the most appropriate experiment to use has become more difficult. This decision must be made carefully to maximize instrument usage and obtain the largest number of couplings with the greatest accuracy possible. Many of the computer programs used in structure calculations can directly apply coupling constant restraints, similar to proton-proton distances developed from NOEs. Therefore, not only is the quality of the structure improved, but the molecular motions (internal dynamics) are better described. In this article, we review the techniques that exist today with particular attention paid to helping the non-expert to choose the appropriate experiment for the problem at hand. In addition, the use of coupling constants in computer simulations are discussed.
    Additional Material: 32 Ill.
    Type of Medium: Electronic Resource
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