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Bioinformatics Tool for Prediction of Protein Solubility
Hronský, Patrik ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
This master's thesis addresses the solubility of recombinant proteins and its prediction. It describes the subject of protein synthesis, as well as the process of recombinant protein creation. Recombinant protein synthesis is of great importance for example to pharmacologic industry. This synthesis is not a simple task and it does not always produce viable proteins. Protein solubility is an important factor, determining the viability of the resulting proteins. It is of course favourable for companies, that take part in recombinant protein synthesis, to focus their effort and their resources on proteins, that will be viable in the end. In this regard, bioinformatics is of great help, as it is capable, with the help of machine learning, of predicting the solubility of proteins, for example based on their sequences. This thesis introduces the reader to the basic principles of machine learning and presents several machine learning methods, used in the field of protein solubility prediction. It deals with the definition of a dataset, which is later used to test selected predictors, as well as to train the ensemble predictor, which is the main focus of this thesis. It also focuses on several specific protein solubility predictors and explains the basic principles upon which they are built, as well as the results of their testing. In the end, it presents the ensemble predictor of protein solubility.
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Expression and purification of adhesive recombinant proteins, sericin 2 and salivary gland secretion 3
VU, Trang Thanh
Recombinant proteins derived from Bombyx mori Ser-2 gene and Drosophila melanogaster Sgs3 gene were expressed in bacterial expression systems, purified and partially characterised. The identity of the expressed recombinant proteins was verified by mass spectroscopy. The recombinant proteins were tested for their ability to coat hydrophobic surfaces and sequentially serve as a substrate for the attachment of cells in tissue culture. The quality of the recombinant protein surface coating was examined by scanning electron microscopy. The results show that further optimisation for the purification, solubilization and refolding of these recombinant proteins is needed to incorporate their potential as biomaterials in the future.
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Bioinformatics Tool for Prediction of Protein Solubility
Hronský, Patrik ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
This master's thesis addresses the solubility of recombinant proteins and its prediction. It describes the subject of protein synthesis, as well as the process of recombinant protein creation. Recombinant protein synthesis is of great importance for example to pharmacologic industry. This synthesis is not a simple task and it does not always produce viable proteins. Protein solubility is an important factor, determining the viability of the resulting proteins. It is of course favourable for companies, that take part in recombinant protein synthesis, to focus their effort and their resources on proteins, that will be viable in the end. In this regard, bioinformatics is of great help, as it is capable, with the help of machine learning, of predicting the solubility of proteins, for example based on their sequences. This thesis introduces the reader to the basic principles of machine learning and presents several machine learning methods, used in the field of protein solubility prediction. It deals with the definition of a dataset, which is later used to test selected predictors, as well as to train the ensemble predictor, which is the main focus of this thesis. It also focuses on several specific protein solubility predictors and explains the basic principles upon which they are built, as well as the results of their testing. In the end, it presents the ensemble predictor of protein solubility.
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