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Visualization of the Chemical Space
Škoda, Petr ; Hoksza, David (advisor) ; Novák, Jiří (referee)
Exploration of chemical space is an important part of the drug discovery pro- cess and its importance grows with computation power which permits to explore greater parts of the chemical space. One of the possibilities of the exploration is vi- sualization. Currently, several method for visualization are implemented but there exists no framework focusing primarily on support of the development of new me- thods. In this work we summarized requirements for such framework and with respect to these requirement we implemented such framework. The framework is modular and offers easy implementation of every single part of the visualization pipeline. The framework incorporates an application that provides graphical in- terface for modules' manipulation and presentation of visualization results. For simple utilization of the application without the necessity of implementation of one's own module, several visualization methods have been implemented. These visualization methods were employed in experimental evaluation on both real and artificial datasets 1
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Scaffold hopping-based exploration of chemical space
Mikeš, Marek ; Hoksza, David (advisor) ; Krivák, Radoslav (referee)
This work is based on the Molpher SW project, which is client-server application aiding exploration of chemical space between two input molecules. Aim of master thesis was modify the current version of program to manage scaffold hopping technique. This technique represents molecule in a simplified way. The simpler molecule is called scaffold. First of all there was need to define seve- ral levels of granularity and for each level define morphing operators. Server was modified with respect for parallelization. Experimental exploration of chemical space with and without the new feature is part of this work too. Powered by TCPDF (www.tcpdf.org)
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Hierarchical visualization of the chemical space
Velkoborský, Jakub ; Hoksza, David (advisor) ; Škoda, Petr (referee)
The purpose of this thesis was to design and implement a hierarchical approach to visualization of the chemical space. Such visualization is a challenging yet important topic used in diverse fields ranging from material engineering to drug design. Especially in drug design, modern methods of high- throughput screening generate large amounts of data that would benefit from hierarchical analysis. One possible approach to hierarchical classification of molecules is a structure based classification based on molecular scaffolds. The scaffolds are widely used by medicinal chemists to group molecules of similar properties. A few scaffold-based hierarchical visualization methods have been proposed. However, to our best knowledge, there exists no tool that would provide a scaffold-based hierarchical visualization of molecular data sets on the background of known chemical space. In this thesis, such tool was created. First, a scaffold tree hierarchy based on ring topologies was designed. Next, this hierarchy was used to analyze frequency of scaffolds extracted from molecules in PubChem Compound database. Subsequently, the PubChem Compound scaffold frequency data was used as a background for visualization of molecular data sets. The visualization is performed by a client-server application implemented as a part of...
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Scaffold hopping-based exploration of chemical space
Mikeš, Marek ; Hoksza, David (advisor) ; Krivák, Radoslav (referee)
This work is based on the Molpher SW project, which is client-server application aiding exploration of chemical space between two input molecules. Aim of master thesis was modify the current version of program to manage scaffold hopping technique. This technique represents molecule in a simplified way. The simpler molecule is called scaffold. First of all there was need to define seve- ral levels of granularity and for each level define morphing operators. Server was modified with respect for parallelization. Experimental exploration of chemical space with and without the new feature is part of this work too. Powered by TCPDF (www.tcpdf.org)
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Visualization of the Chemical Space
Škoda, Petr ; Hoksza, David (advisor) ; Novák, Jiří (referee)
Exploration of chemical space is an important part of the drug discovery pro- cess and its importance grows with computation power which permits to explore greater parts of the chemical space. One of the possibilities of the exploration is vi- sualization. Currently, several method for visualization are implemented but there exists no framework focusing primarily on support of the development of new me- thods. In this work we summarized requirements for such framework and with respect to these requirement we implemented such framework. The framework is modular and offers easy implementation of every single part of the visualization pipeline. The framework incorporates an application that provides graphical in- terface for modules' manipulation and presentation of visualization results. For simple utilization of the application without the necessity of implementation of one's own module, several visualization methods have been implemented. These visualization methods were employed in experimental evaluation on both real and artificial datasets 1
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