Thesis Details

Computational Workflow for the Prediction and Design of Stable Proteins

Master's Thesis Student: Kadleček Josef Academic Year: 2021/2022 Supervisor: Musil Miloš, Ing., Ph.D.
Czech title
Výpočetní metoda pro predikci a konstrukci stabilních proteinů
Language
English
Abstract

This thesis focuses on enriching computational tools for the prediction of protein mutations for the purpose of enriching their stability. Stable mutants of proteins are necessary for the development of the new drugs. Unfortunately, experimental validation of the stabilization effect of given mutations is costly and time demanding. Therefore, the FireProt tool was developed.  FireProt utilizes a combination of both evolutionary and energy-based approaches for identifying potentially stabilizing mutations. This thesis enriches the FireProt tool with the possibility of entering custom mutations for the analysis. It also integrates other prediction software, FireProt ASR, and provides user with an option to select multiple mutational strategies for the detection of stabilizing mutations. Furthermore, it enriches the FireProt tool with another information about proteins residues (for instance relative B-factor) and makes it possible to utilize homology modeling to model the protein's structure based on its sequence. Lastly, it introduces a novel approach for the design of multiple-point mutants.

Keywords

Protein engineering, amino acid mutation, protein stability, stability prediction, multiple-point mutants

Department
Degree Programme
Files
Status
defended, grade A
Date
21 June 2022
Reviewer
Committee
Sekanina Lukáš, prof. Ing., Ph.D. (DCSY FIT BUT), předseda
Bidlo Michal, Ing., Ph.D. (DCSY FIT BUT), člen
Burgetová Ivana, Ing., Ph.D. (DIFS FIT BUT), člen
Lengál Ondřej, Ing., Ph.D. (DITS FIT BUT), člen
Matoušek Radomil, doc. Ing., Ph.D. (IACS FME BUT), člen
Vašíček Zdeněk, doc. Ing., Ph.D. (DCSY FIT BUT), člen
Citation
KADLEČEK, Josef. Computational Workflow for the Prediction and Design of Stable Proteins. Brno, 2022. Master's Thesis. Brno University of Technology, Faculty of Information Technology. 2022-06-21. Supervised by Musil Miloš. Available from: https://www.fit.vut.cz/study/thesis/24648/
BibTeX
@mastersthesis{FITMT24648,
    author = "Josef Kadle\v{c}ek",
    type = "Master's thesis",
    title = "Computational Workflow for the Prediction and Design of Stable Proteins",
    school = "Brno University of Technology, Faculty of Information Technology",
    year = 2022,
    location = "Brno, CZ",
    language = "english",
    url = "https://www.fit.vut.cz/study/thesis/24648/"
}
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