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Methods for prediction of secondary structure in proteins
Hoštáková, Nina ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
The examination of protein structure is crucial in determining protein function in organism. This work deals with the issue of 1D, 2D and 3D structures, into which are proteins organized in space. Emphasis is placed on secondary structure, which can be predicted directly from the amino acid sequences and then used for the estimation of spatial structure. On this procedure are focused computational methods, using algorithms that convert the order of amino acids into the order of preferences for secondary structures. To direct determination of the structure by creating structural models is devoted chapter Experimental Methods (NMR spectroscopy, RTG crystallography). The main aim of this work is practical realization of protein secondary structure prediction method. The created program is supplemented by graphical user interface. In the final part the results of the program based on Chou- Fasman method are compared to the outputs of freely available softwares from the Internet.
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Flow detection using optical intereference methods
Hoštáková, Nina ; Štohanzlová, Petra (referee) ; Kolář, Radim (advisor)
The thesis deals with LSCI (Laser Speckle Contrast Imaging), an optical method utilizing laser speckle contrast for the estimation of blood flow changes. LSCI is non-invasive and technically not demanding approach, capabilities of which have not yet been fully exploited. The literature review part contains detailed description of the operating principle, imaging techniques, potential for medical applications with considering the limiting factors. The main aim of the thesis is to design and construct a complete LSCI system including appropriate phantoms able to simulate blood flow through the tissue. Imaging algorithms for the obtained data evaluation were implemented in Matlab® development enviroment. Finally, the created system was tested using different acquisition parameters as well as varying the image processing schemes. The resulting qualitative flow images were subsequently discussed and confronted with the theoretical assumptions.
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Methods for prediction of secondary structure in proteins
Hoštáková, Nina ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
The examination of protein structure is crucial in determining protein function in organism. This work deals with the issue of 1D, 2D and 3D structures, into which are proteins organized in space. Emphasis is placed on secondary structure, which can be predicted directly from the amino acid sequences and then used for the estimation of spatial structure. On this procedure are focused computational methods, using algorithms that convert the order of amino acids into the order of preferences for secondary structures. To direct determination of the structure by creating structural models is devoted chapter Experimental Methods (NMR spectroscopy, RTG crystallography). The main aim of this work is practical realization of protein secondary structure prediction method. The created program is supplemented by graphical user interface. In the final part the results of the program based on Chou- Fasman method are compared to the outputs of freely available softwares from the Internet.
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Flow detection using optical intereference methods
Hoštáková, Nina ; Štohanzlová, Petra (referee) ; Kolář, Radim (advisor)
The thesis deals with LSCI (Laser Speckle Contrast Imaging), an optical method utilizing laser speckle contrast for the estimation of blood flow changes. LSCI is non-invasive and technically not demanding approach, capabilities of which have not yet been fully exploited. The literature review part contains detailed description of the operating principle, imaging techniques, potential for medical applications with considering the limiting factors. The main aim of the thesis is to design and construct a complete LSCI system including appropriate phantoms able to simulate blood flow through the tissue. Imaging algorithms for the obtained data evaluation were implemented in Matlab® development enviroment. Finally, the created system was tested using different acquisition parameters as well as varying the image processing schemes. The resulting qualitative flow images were subsequently discussed and confronted with the theoretical assumptions.
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