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Prediction of ligand binding sites from protein structure
Krivák, Radoslav ; Hoksza, David (advisor) ; Berka, Karel (referee) ; Brezovský, Jan (referee)
Ligand binding site prediction from protein structure is a fundamental prob- lem in the field of structural bioinformatics that has many applications related to the elucidation of protein function and structure-based drug discovery. The first focus of this thesis was the application of machine learning to this and related problems. The second focus was the development of practically usable tools based on our research. The machine learning based tools produced as a result of the work on this thesis include the pocket re-scoring method PRANK, a stand-alone ligand binding site prediction method P2Rank (together with its extended web interface PrankWeb) and the peptide binding prediction method P2Rank-Pept. We have shown that our methods outperformed available state- of-the-art tools while providing other benefits like prediction speed and stability. Furthermore, we have developed AHoJ, a flexible tool for the search and align- ment of Apo-Holo protein pairs in the PDB. AHoJ that is ideal for creating Apo-Holo datasets which can in turn help to better evaluate binding site pre- diction methods in the future. 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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Web Based Issue Tracker
Krivák, Radoslav ; Poch, Tomáš (advisor) ; Libič, Peter (referee)
The present work deals with the analysis, design and implementation of an issue tracking system with web interface. The introduction is to explain what an issue tracker is and what are the bene ts of its deployment in the organization or company. Consequently, new solution is designed and described with the help of usecases. The work brings an overview of technologies and patterns used in Java web application development. Architecture of the application and the way selected technologies are used is described. The main part of the work is the implementation of the application itself in the Java language with the help of Struts2, Spring, Hibernate and Lucene technologies.
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Platform for benchmarking efficiency of molecular similarities
Patík, Vladimír ; Škoda, Petr (advisor) ; Krivák, Radoslav (referee)
In the bachelor thesis I designed and developed a platform for testing of the ligand-based virtual screening (LBVS) methods, which allows communication via web sites, running tests on the Metacentrum infrastructure or remote computers for speeding up the processing of tests, adding own data-sets and LBVS methods. Several basic methods are attached to the program and two packages of basic datasets can be downloaded from the Internet sources mentioned in the text. The use of the platform has been verified in two exemplary use cases. The first goal was to replicate and verify the accuracy of the published experiment. The second example was the comparison of method based on the count of atoms in molecule with the RDKit library methods. 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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Algorithms for protein-ligand binding site discovery
Krivák, Radoslav ; Neruda, Roman (advisor) ; Mráz, František (referee)
Virtually all processes in living organisms are conducted by proteins. Proteins perform their function by binding to other proteins (protein-protein interactions) or small molecules - so called ligands (protein-ligand interactions). Active sites for protein-ligand interactions are pockets in protein structure where ligand can bind. Predicting of ligand binding sites is the first step to study and predict protein functions and structure based drug-design. In this thesis we reviewed current approaches for binding site prediction and proposed our own improvement. We have developed a novel pocket ranking function based on prediction model that predicts ligandability (ability to bind a ligand) of a given point inside of a pocket. Prediction is done considering only a local physicochemical and geometric properties derived from neighbourhood.
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Web Based Issue Tracker
Krivák, Radoslav ; Libič, Peter (referee) ; Poch, Tomáš (advisor)
The present work deals with the analysis, design and implementation of an issue tracking system with web interface. The introduction is to explain what an issue tracker is and what are the bene ts of its deployment in the organization or company. Consequently, new solution is designed and described with the help of usecases. The work brings an overview of technologies and patterns used in Java web application development. Architecture of the application and the way selected technologies are used is described. The main part of the work is the implementation of the application itself in the Java language with the help of Struts2, Spring, Hibernate and Lucene technologies.
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