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Clustering of Protein Sequences Based on Primary Structure of Proteins
Jurásek, Petr ; Stryka, Lukáš (referee) ; Burgetová, Ivana (advisor)
This master's thesis consider clustering of protein sequences based on primary structure of proteins. Studies the protein sequences from they primary structure. Describes methods for similarities in the amino acid sequences of proteins, cluster analysis and clustering algorithms. This thesis presents concept of distance function based on similarity of protein sequences and implements clustering algorithms ANGES, k-means, k-medoids in Python programming language.
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Analysis of the Tools for Detecting Similarities between Tertiary Protein Structures
Trlica, Jiří ; Vogel, Ivan (referee) ; Bendl, Jaroslav (advisor)
Alignment of the three-dimensional structures of proteins is an essential task in bioinformatics. Because there are many tools offering this functionality, only a limited subset of them was chosen for comparison (DALI, LOCK 2, SPALIGN, MUSTANG and CLICK). These tools vary in the principle of calculation. Their performance was measured on three proteins, which represent main protein classes (all-α, all-β, α/β). These proteins were tested against a subset of PDB database containing 2 357 records. The results were visualized by ROC curves and the tools were compared by their area under ROC curve (AUC metric). According to this metric, the best results were obtained for SPALIGN.
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Protein Classification Techniques
Dekrét, Lukáš ; Zendulka, Jaroslav (referee) ; Burgetová, Ivana (advisor)
Main goal of classifying proteins into families is to understand structural, functional and evolutionary relationships between individual proteins, which are not easily deducible from available data. Since the structure and function of proteins are closely related, determination of function is mainly based on structural properties, that can be obtained relatively easily with current resources. Protein classification is also used in development of special medicines, in the diagnosis of clinical diseases or in personalized healthcare, which means a lot of investment in it. I created a new hierarchical tool for protein classification that achieves better results than some existing solutions. The implementation of the tool was preceded by acquaintance with the properties of proteins, examination of existing classification approaches, creation of an extensive data set, realizing experiments and selection of the final classifiers of the hierarchical tool.
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Development of selected CD markers and their role in the phylogenesis of human immune system
Podolská, Tereza ; Růžičková, Šárka (advisor) ; Vinkler, Michal (referee)
In the first part of the thesis we investigated the origin of selected surface CD markers of human, namely CD19, CD20, CD21, CD24, CD27 and CD38 molecules. In addition, nucleotide and amino acid sequences of these molecules were compared using in silico approach. Bioinformatic databases of sequences of selected molecules at DNA, mRNA and protein level, such as GeneBank, NCBI BLAST, Homologene and OrthoDB, have been used. The intent was to identify at the domain level the first organism in which it is possible to find the searched molecule. At the N-terminal domain of the CD38 of birds, a sequence showing significant similarity to the archaebacterial flagellin domain was found. This flagellin sequence in the CD38 avian molecule is located in the region of transmembrane domain, indicating that the occurrence of this sequence might be related to the formation of the transmembrane domain. The approach used here could be implemented in comparative hybridization studies as a tool in the preparatory non-laboratory phase of the research of the presence of paralogs and orthologs in phylogenetically old species. Keywords: CD marker, immunocyte, B lymphocyte, innate and adaptive immunity, sequence database, amino acid, nucleotide
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Protein Classification Techniques
Dekrét, Lukáš ; Zendulka, Jaroslav (referee) ; Burgetová, Ivana (advisor)
Main goal of classifying proteins into families is to understand structural, functional and evolutionary relationships between individual proteins, which are not easily deducible from available data. Since the structure and function of proteins are closely related, determination of function is mainly based on structural properties, that can be obtained relatively easily with current resources. Protein classification is also used in development of special medicines, in the diagnosis of clinical diseases or in personalized healthcare, which means a lot of investment in it. I created a new hierarchical tool for protein classification that achieves better results than some existing solutions. The implementation of the tool was preceded by acquaintance with the properties of proteins, examination of existing classification approaches, creation of an extensive data set, realizing experiments and selection of the final classifiers of the hierarchical tool.
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Adsorption of low molecular weight algal organic matter onto activated carbon during water treatment
Fialová, Kateřina ; Pivokonský, Martin (advisor) ; Kopecká, Ivana (referee)
This diploma thesis deals with the study of adsorption of low-molecular components of organic substances produced by phytoplankton - AOM (Algal Organic Matter) on AC (Activated Carbon) during drinking water treatment. For the experimental purpose in this thesis, there were used selected amino acids as low molecular substances of AOM that are difficult to remove by conventional water treatment process by coagulation. As adsorbent, there was used a detailed characterized of granulated activated carbon (GAC) - Filtrasorb TL 830 (FTL830) which is intended directly for the purpose of water treatment. There were realizing the equilibrium batch adsorption experiments with three different model amino acids - arginine (Arg), phenylalanine (Phe) and aspartic acid (Asp). There was investigated the efficiency of removing amino acid depending on the solution temperature and pH. Results of the adsorption experiments have shown that the temperature affects the adsorption efficiency. Adsorption is essentially described as an exothermic process but the adsorption of Arg and Phe from an aqueous solution to GAC occurs more efficiently at higher temperatures. It means that the adsorption is the endothermic process. In the case of Arg adsorption, the temperature was found to influence adsorption efficiency less than...
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