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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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Measuring of conformational properties of nucleic acids
Hrazdilová, Ivana ; Renčiuk,, Daniel (referee) ; Maděránková, Denisa (advisor)
This thesis gives a brief characteristic of the most important conformations of nucleic acids. It describes alternative conformations that are different from canonical B-DNA helix, such as A-DNA, Z-DNA, triplex structures, or guanine and cytozin quadruplex structures. In the next part it presents most common methods used for determing secondary structure of nucleic acids, which are nuclear magnetic resonance (NMR), measurement of circular dichroism (CD), X-ray diffraction, computational methods, measurements of ultraviolet absorbance and its utilization for analysis of thermal melting curves. In MATLAB was created algorithm with graphical user interface, which analyze melting curves and graphically computes thermodynamic parameters, which are melting temperature and transition enthalpy, which defines stability of examined sample.
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Web Server for Protein Secondary Structure Prediction
Villem, Lukáš ; Očenášek, Pavel (referee) ; Burgetová, Ivana (advisor)
This master’s thesis deals with protein secondary structure prediction. There is a theoretical introduction followed by study of available tools, proposal and implementation of web application, which combines functionality of several web tools used to predict secondary structure. User is asked to choose prediction methods and insert input sequence as plain text or upload a file. Results collected from selected tools serve to convert data into common format, show the result and create new type of prediction. Finally, the testing is applied and influences of tools are adjusted in order to increase percentage of prediction. The output of application is a result of prediction also available as plain text or as a file.
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Quadruplex Detection in DNA Sequences
Sečka, Martin ; Lexa, Matej (referee) ; Martínek, Tomáš (advisor)
This master's thesis focuses on search for sequences potentially forming quadruplexes in DNA sequences, their visualization and filtration. For this purpose a web application was created in cooperation with the Institute of biophysics of Academy of science of Czech republic. This application uses a newly created algorithm able to find all possible formations of quadruplex within given input sequence. Design and implementation of this algorithm are also part of this thesis.
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RNA secondary structure conservation identification module for rPredictor
Pešek, Jan ; Hoksza, David (advisor) ; Škoda, Petr (referee)
The issue of comparing ribosomal RNA secondary structures is currently an open research problem. Goal of this work is to design and implement program comparing so called mutual conservancy of a group of rRNA secondary structures. This program is included as a new module of an existing system called rPredictor consisting of the structure database and an algorithm that predicts these structures. This thesis covers an introduction into the problem of secondary structures conservancy identification and summarizes known approaches towards the problem. The result of this work is a stand alone program for the secondary structure comparison and also a new analytic module of the rPredictor system, where the secondary structure comparison program can be used for comparison of the structures from the rPredictor database. Powered by TCPDF (www.tcpdf.org)
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Web-based tool for RNA secondary structure visualization
Saksa, Jakub ; Hoksza, David (advisor) ; Škoda, Petr (referee)
Visualization of RNA secondary structure is an open problem because there does not exist a well- defined description of the layout process. The layout accepted by the community is habitual. The approach implemented by the Traveler tool, developed at Department of Software Engineering MFF UK, is based on using existing structure with known layout as a template for laying out structure with unknown layout. The first version of the program had few issues that made it difficult to use. The goal of the thesis was to improve Traveler so that the tool is more accessible. Improvements include ability to process pseudoknots, intermediate format for images of secondary structures and modification of the layout-creating algorithm. We created a web application that serves as an user interface for Traveler. The application is able to automatically choose a template for the structure too.
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Protein secondary structure prediction using deep neural networks
Filippi, Michal ; Hoksza, David (advisor) ; Matzner, Filip (referee)
Determination of protein structure in space is a crucial part of protein function analysis. But structure determination is an expensive and time consuming pro- cess, therefore structure prediction model raised on popularity. The most notable subproblem of protein structure prediction is prediction of local conformation of the adjacent amino acids, ie. secondary structure. This thesis studies usage of deep neural networks for protein secondary structure prediction. We implemented pre- diction model and different modifications are evaluated. Especially compassion of LSTM and GRU memory cells was done. Furthermore, two new preprocessing me- thods are evaluated. Fast PSSM calculation method was proposed and prediction of tertiary structure was used as input for prediction model. Last part of this thesis examine application of filtering methods for models predicting secondary structure with eight classes. 1
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