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National Repository of Grey Literature 2 records found  Search took 0.00 seconds. 
Identification of the Protein Tunnels Using Molecular Dynamics
 Kohout, Petr ; Martínek, Tomáš (referee) ; Musil, Miloš (advisor)
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.
Detailed record
Identification of the Protein Tunnels Using Molecular Dynamics
 Kohout, Petr ; Martínek, Tomáš (referee) ; Musil, Miloš (advisor)
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.
Detailed record

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