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Geometry of protein moleculs
Novotný, Jan ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
Objective of this work was to study the spatial arrangement of protein molecules, with their extraction, notations and variables used in the course descriptions. Prediction of protein structures is very important for determining the future function of proteins. Another objective was to create a function in MATLAB that will graphically represent the spatial arrangement of the backbone structure of the protein by form Ramachandran plot. Along with this function create another function to render the side-chains of amino acids and function to calculate the stereochemical quality. Finally, create a program for a complete assessment of the spatial arrangement of the protein molecules and calculating the stereochemical quality of and test program for protein structures from public databases RSCB PDB.
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Analysis of Protein Structure Visualisation Tools
Klemšová, Jarmila ; Jaša, Petr (referee) ; Burgetová, Ivana (advisor)
In this thesis we analyze several tools for protein structure visualisation. We describe the structure of the proteins, the databases for storing protein structures and their data formats. Next part of the thesis, provides detailed information about selected visualisation tools and some scripts for them. The thesis also include an example of visualisation of the selected protein.
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Techniques for Comparing Biological Sequences
Sladký, Roman ; Křivka, Zbyněk (referee) ; Burgetová, Ivana (advisor)
This work presents the building up of basic biological units DNA, RNA and proteins as well as their function. Provided data are kept in biological databases which are connected worldwide to supply preferable communication along with all kinds of available information to be used in the scientific research. The secret of alive is hidden in genes coded in sequences of nucleotides. Genes enable the creation of proteins which are made of sequences of amino-acids. The wide-spread methods of comparing these sequences are FASTA and BLAST algorithms. Their base is used for the PSProt program which is described in this work. PSProt program is the tool for comparing the sequences of proteins. First it is necessary to synthesise the protein from the DNA oligonucleotide because it codes the surveyed protein. The most similar proteins are searched out by heuristic of hitpoints, then their final score that is essential for aligning is modified by semiglobal alignment algorithm.
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Prediction of the Effect of Mutation on Protein Solubility
Velecký, Jan ; Martínek, Tomáš (referee) ; Hon, Jiří (advisor)
The goal of the thesis is to create a predictor of the effect of a mutation on protein solubility given its initial 3D structure. Protein solubility prediction is a bioinformatics problem which is still considered unsolved. Especially a prediction using a 3D structure has not gained much attention yet. A relevant knowledge about proteins, protein solubility and existing predictors is included in the text. The principle of the designed predictor is inspired by the Surface Patches article and therefore it also aims to validate the results achieved by its authors. The designed tool uses changes of positive regions of the electric potential above the protein's surface to make a prediction. The tool has been successfully implemented and series of computationally expensive experiments have been performed. It was shown that the electric potential, hence the predictor itself too, can be successfully used just for a limited set of proteins. On top of that, the method used in the article correlates with a much simpler variable - the protein's net charge.
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Bioinformatics Tool for Protein Structure Prediction
Plaga, Michal ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
The goal of this thesis is test and comparation of the offline tools for prediction of protein structure and creation of metaprediktor, which allows the user to select the appropriate tool, according to given parameters. Testing tool is based on a dataset of proteins, which is based on the SCOP database and it is trying to be as balanced as possible to include proteins from different families and thus could best evaluate individual tools. The results of this thesis are requirements of metaprediktor and also which data and settings can be allowed and processed and how it will be implemented.
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Protein Structure Prediction
Tuček, Jaroslav ; Martínek, Tomáš (referee) ; Burgetová, Ivana (advisor)
This work describes the three dimensional structure of protein molecules and biological databases used to store information about this structure or its hierarchical classification. Current methods of computational structure prediction are overviewed with an emphasis on comparative modeling. This particular method is also implemented in a proof-of-concept program and finally, the implementation is analysed.
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Attributes Calculating for Prediction of Effects of Mutation on Protein Function
Matějíček, Jiří ; Burgetová, Ivana (referee) ; Jaša, Petr (advisor)
This bachelor thesis deals with the bioinformatics techniques for the acquisition of attributes useful for prediction of mutation effects on the protein function. The work primarily aims to develop a user-friendly application for calculation of attributes of mutations from the protein sequence and structure. The developed application serves for integration of specialized tools such as FoldX. The standardized interface enables to implement additional computational tools and collect a diverse set of attributes from different sources. These attribute sets can then serve as an input for different prediction methods and help to improve predictions of mutation effects.
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Difference in amino acid distribution in sequences of structured and unstructured proteins
Sotáková, Patrícia ; Vondrášek, Jiří (advisor) ; Sanchez Rocha, Alma Carolina (referee)
Disordered proteins are a topic of growing interest. With ongoing research describing the relationship between sequence and structure, this work aims to investigate features in an amino acid sequence that could indicate finger- prints of structured or disordered proteins. These fingerprints could deepen our understanding of disordered regions or protein folding. Furthermore, this knowledge could help design new deep-learning predictors of protein dis- order or protein domain recognition. Statistical analysis was performed on sequences obtained from Protein Data Bank and DisProt database, including a comparison of protein sequences with artificial ones generated under the assumption of amino acid pairwise independence. Subsequently, we identified triples of two amino acids and their distance that are significantly different in occurrence to the artificial set. Based on this analysis, we sorted the triples into the following categories: overestimated, random, and underesti- mated. Observed pairs with abnormal frequency in a given distance can be interpreted as a fingerprint of secondary structure, motif, domain, or other unknown identification of disordered proteins depending on the dataset. A simple example of a sequence fingerprint was observed in the PDB dataset; the abundance of histidines in...
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Framework for retrieval and analysis of proteins apo and holo forms from PDB
Král, Adam ; Hoksza, David (advisor) ; Sanchez Rocha, Alma Carolina (referee)
We developed a software framework that allows the analysis of ligand-free (apo) and ligand-bound (holo) forms of proteins that are accessible in PDB. The software downloads the current version of the PDB, divides the structures into groups of the same molecules, and these into apo and holo forms. Finally, it is possible to analyze pairs of apo and holo structures with respect to their different structural characteristics. In addition to the software work itself, we also verify results against previous work on an equivalent dataset, and obtain results for the current version of PDB. Keywords: protein; structural bioinformatics; PDB
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Framework for retrieval and analysis of proteins apo and holo forms from PDB
Král, Adam ; Hoksza, David (advisor) ; Novotný, Marian (referee)
We developed a software framework that allows the analysis of ligand-free (apo) and ligand-bound (holo) forms of proteins that are accessible in PDB. The software downloads the current version of the PDB, divides the structures into groups of the same molecules, and these into apo and holo forms. Finally, it is possible to analyze pairs of apo and holo structures with respect to their different structural characteristics. In addition to the software work itself, we present the results of selected analyses of the current version of the data in the PDB. We also verify the results against previous work.
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