Thesis Details

Identifikace proteinových tunelů s využitím molekulárních dynamik

Master's Thesis Student: Kohout Petr Academic Year: 2021/2022 Supervisor: Musil Miloš, Ing., Ph.D.
English title
Identification of the Protein Tunnels Using Molecular Dynamics

This thesis focuses on the analysis of protein structures. The aim is to design Caver Web 2.0 -- a new version of the web application that integrates additional scientific tools and allows users to go through a complicated workflow to provide relevant results without the need for a deeper knowledge of the integrated tools. Everything will be delivered through a simple and interactive user interface. The application extends the original Caver Web 1.0 application with new features. Caver Web 1.0 is a web server suitable for identifying protein tunnels and channels for which it allows to run ligand transport analyses. The program is characterized by an intuitive and user-friendly interface with minimum required input from the user. The server is suitable for researchers without advanced bioinformatics or technical knowledge. Its current version is well established and highly used in the scientific community (35,000 completed calculations in two years of operation). The most significant limitation of the current version is the ability to analyze only static structure, which often provides an incomplete biological picture. Therefore, it was decided to extend the tool to calculate molecular dynamics to provide a comprehensive picture of protein structure changes.


bioinformatics, web application, protein engineering, molecular dynamics, protein tunnels, ligand docking

Degree Programme
defended, grade A
21 June 2022
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
KOHOUT, Petr. Identifikace proteinových tunelů s využitím molekulárních dynamik. Brno, 2022. Master's Thesis. Brno University of Technology, Faculty of Information Technology. 2022-06-21. Supervised by Musil Miloš. Available from:
    author = "Petr Kohout",
    type = "Master's thesis",
    title = "Identifikace proteinov\'{y}ch tunel\r{u} s vyu\v{z}it\'{i}m molekul\'{a}rn\'{i}ch dynamik",
    school = "Brno University of Technology, Faculty of Information Technology",
    year = 2022,
    location = "Brno, CZ",
    language = "czech",
    url = ""
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