Browsing by Author "Fredriksson, Jonas"

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Algorithms for analysis of NMR projections: Design, implementation and applications
(2011-03-29) Fredriksson, Jonas
With an increasing rate of protein expressions the need for fast protein characterization has become more important. Protein NMR has long been an important contributor for protein characterization; being one of a few techniques that can study proteins at atomic resolution in their native state. Whitin recent years faster experimental and processing methods have emerged that are now becoming routine. This thesis describes algorithms for automatic backbone assignment and validation of structure information by using projection experiments together with a decomposition method. Projection experiments reduce measurement time for multidimensional spectra thus making it possible to obtain very high dimensional spectral information in a fraction of the time required for a conventional experiment. By combining different experiments backbone, side chain and NOE information can be obtained. A set of software tools for automatic backbone characterization where developed from the implementation of different algorithms in conjunction with different proteins and projection experiments. Testing and refinement of the different tools resulted in a robust characterization method well suited for different proteins. Possible future projects are expanding the methods to side chain and structure determination making the characterization more complete.
deco - A decomposition program for NMR projection experiments
(2012-09-18) Fredriksson, Jonas; Göteborgs universitet/Institutionen för data- och informationsteknik; University of Gothenburg/Department of Computer Science and Engineering
In protein NMR high dimensional spectra are difficult to measure because long measurement times and low signal to noise. To overcome this barrier fast acquisition techniques have been developed. One of these is projection experiments that uses coupled evolution periods instead of using independent evolution periods. This reduces measurement time dramatically but has constraints in terms of protein size because of low signal to noise present in high dimensional spectra. Analyzing these spectra requires software tools that can process the convoluted spectra and assign the resulting signals. In this thesis a new algorithm is presented for decomposing convoluted spectra using python as a model and Fortran routines for steps that are time critical. All test where done on the azurin and the ubiquitin protein. and the result is a software tool for resolving projection experiments using a new algorithm together with a graphical user interface.
deco - A decomposition program for NMR projection experiments
(2012-08-13) Fredriksson, Jonas; Göteborgs universitet/Institutionen för data- och informationsteknik; University of Gothenburg/Department of Computer Science and Engineering
In protein NMR high dimensional spectra are difficult to measure because long measurement times and low signal to noise. To overcome this barrier fast acquisition techniques have been developed. One of these is projection experiments that uses coupled evolution periods instead of using independent evolution periods. This reduces measurement time dramatically but has constraints in terms of protein size because of low signal to noise present in high dimensional spectra. Analyzing these spectra requires software tools that can process the convoluted spectra and assign the resulting signals. In this thesis a new algorithm is presented for decomposing convoluted spectra using python as a model and Fortran routines for steps that are time critical. All test where done on the azurin and the ubiquitin protein. and the result is a software tool for resolving projection experiments using a new algorithm together with a graphical user interface.