Abstract
Relaxation dispersion spectroscopy is one of the most widely used techniques for the analysis of protein dynamics. To obtain a detailed understanding of the protein function from the view point of dynamics, it is essential to fit relaxation dispersion data accurately. The grid search method is commonly used for relaxation dispersion curve fits, but it does not always find the global minimum that provides the best-fit parameter set. Also, the fitting quality does not always improve with increase of the grid size although the computational time becomes longer. This is because relaxation dispersion curve fitting suffers from a local minimum problem, which is a general problem in non-linear least squares curve fitting. Therefore, in order to fit relaxation dispersion data rapidly and accurately, we developed a new fitting program called GLOVE that minimizes global and local parameters alternately, and incorporates a Monte-Carlo minimization method that enables fitting parameters to pass through local minima with low computational cost. GLOVE also implements a random search method, which sets up initial parameter values randomly within user-defined ranges. We demonstrate here that the combined use of the three methods can find the global minimum more rapidly and more accurately than grid search alone.
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Acknowledgments
This work was supported by a Grant-in-Aid for Scientific Research on Innovative Areas (to K.S.) from the MEXT of Japan and by grant GM075995 (to P.E.W.) from the National Institutes of Health. J.L. was supported by postdoctoral fellowship grant PF-05-056-01 from the American Cancer Society. GLOVE is available upon request to the authors.
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Sugase, K., Konuma, T., Lansing, J.C. et al. Fast and accurate fitting of relaxation dispersion data using the flexible software package GLOVE. J Biomol NMR 56, 275–283 (2013). https://doi.org/10.1007/s10858-013-9747-5
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DOI: https://doi.org/10.1007/s10858-013-9747-5