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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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Analysis of selected secondary structures of nucleic acids
Skružný, Petr ; Mokrejš, Martin (advisor) ; Drda Morávková, Alena (referee)
This work introduces a database of experimentally verified structures of nucleic acids which were collected from published scientific literature. The database is annotated and the structures are analysed from the perspective of quality and it was found that the experimentally obtained data are not always sufficient - their supporting evidence is often limited and their quality is not convincing. This work also discusses some of the problems, that can be encountered when the structures are experimentally probed. Contents of the database were compared to the RFAM database and despite of its small range it contains 80 new structures. The complete database of 166 structures can be possibly used to optimise software used to predict derived structures of nucleic acids. Furthermore, the work presents several possible ways of improvement of the quality of contained structures.
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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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Effects of phosphorylation on 3D conformation of proteins
Tomčalová, Brenda ; Novotný, Marian (advisor) ; Vymětal, Jiří (referee)
Phosphorylation is one of the most ubiquitous posttranslational modification types. Understanding of itsfunction and regulation has significant impact on diagnosis and treatment of many diseases. This thesis presents and summarizes the results of several publications that analyze phosphorylation on large datasets using bioinformatics tools. In this thesis the general principles how the phosphorylation influences physico-chemical properties of proteins are described. In the first and the second chapter the evolution principles, function and regulation of protein kinases and phosphatases are provided. In the third chapter thesis concentrates on the distributions of phosphorylated sites among organisms (plants and animals). In the last chapter current knowledge of orthosteric and allosteric effects of phosphorylation as well as its effects on 2D and 3D structure of phosphorylated proteins is summarized.
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