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Interaction of proteins with inhibitors: quantum chemical study
Dobeš, Petr ; Hobza, Pavel (advisor) ; Vondrášek, Jiří (referee) ; Jurečka, Petr (referee)
This dissertation focuses on theoretical studies of the interaction between protein kinases and their inhibitors. Studied protein kinases, cyclin-dependent kinase 2 (CDK2) and CK2 kinase (casein kinase 2) play an important role in regulating cellular processes in eukaryotic organisms. Their abnormal function in human cells can lead to serious diseases. This process can be stopped by blocking the aberrant protein kinases using specific low molecular weight inhibitors. Inhibitors of protein kinases typically bind to the active site of the enzyme by noncovalent interactions. Theoretical description of these interactions using quantum-chemical and molecular mechanical methods can help in understanding the biophysical principles governing the binding. These, in turn, can be subsequently used for a rational drug design of more effective and more specific inhibitors. The stabilization energy of the complex of CDK2 with inhibitor roscovitine is predominantly formed by the dispersion energy. DFT methods, which do not describe the dispersion energy was thus completely inappropriate for the treatment of such a system. When an empirical term is included to correct for the description of dispersion, such methods, as e.g. the SCC-DFTB-D, can be recommended for computation of this or similar complexes. The dominant part...
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Principles of application of fluid inclusions for the study of hydrothermal mineralizations
Štrba, Martin ; Zachariáš, Jiří (advisor) ; Dobeš, Petr (referee)
The bachelor thesis is subdivided into two review parts and one experimental part. The first part focuses on petrography and microthermometric study of fluid inclusions. Petrography chapter lists genetic types of inclusions, and various mechanisms that determine their shape and digree of fill. Emphasis is placed especially on the microthermometric study of fluid inclusions. The phase changes in H2O - NaCl and H2O - CO2 - salts systems at low and high temperatures are described in detail. A separate chapter is dedicated to interpretation of microthermometric data and to their use in determination of pressure-temperature conditions of minerals formation. The second part of the thesis lists several examples of using the fluid inclusions in the study of hydrothermal deposits and in prospecting of ore deposits (Pb - Zn - fluorite deposits of Mississippi valley type, porphy - type, Cu - ores at Bingham). One chapter is dedicated to Bleïda deposit (Morocco), Kanmantoo deposit (Australia) and San Cristobal vein (Peru). This chapter discribes geology, mineralogy and fluid inclusion data of these deposits. Third, experimental, chapter deals with hydrothermal mineralization in the Ševětín quarry. It includes the regional geology of Ševětín massif, geology of the quarry and the mineralogy of hydrothermal...
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OCR Trained with Unanotated Data
Buchal, Petr ; Dobeš, Petr (referee) ; Hradiš, Michal (advisor)
The creation of a high-quality optical character recognition system (OCR) requires a large amount of labeled data. Obtaining, or in other words creating, such a quantity of labeled data is a costly process. This thesis focuses on several methods which efficiently use unlabeled data for the training of an OCR neural network. The proposed methods fall into the category of self-training algorithms. The general approach of all proposed methods can be summarized as follows. Firstly, the seed model is trained on a limited amount of labeled data. Then, the seed model in combination with the language model is used for producing pseudo-labels for unlabeled data. Machine-labeled data are then combined with the training data used for the creation of the seed model and they are used again for the creation of the target model. The successfulness of individual methods is measured on the handwritten ICFHR 2014 Bentham dataset. Experiments were conducted on two datasets which represented different degrees of labeled data availability. The best model trained on the smaller dataset achieved 3.70 CER [%], which is a relative improvement of 42 % in comparison with the seed model, and the best model trained on the bigger dataset achieved 1.90 CER [%], which is a relative improvement of 26 % in comparison with the seed model. This thesis shows that the proposed methods can be efficiently used to improve the OCR error rate by means of unlabeled data.
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Anticurtaining - Image Filter for Electron Microscopy
Dvořák, Martin ; Dobeš, Petr (referee) ; Zemčík, Pavel (advisor)
Tomographic analysis produces 3D images of examined material in nanoscale by focus ion beam (FIB). This thesis presents new approach to elimination of the curtain effect by machine learning method. Convolution neuron network is proposed for elimination of damaged imagine by the supervised learning technique. Designed network deals with features of damaged image, which are caused by wavelet transformation. The outcome is visually clear image. This thesis also designs creation of synthetic data set for training the neuron network which are created by simulating physical process of the creation of the real image. The simulation is made of creation of examined material by milling which is done by FIB and by process displaying of the surface by electron microscope (SEM). This newly created approach works precisely with real images. The qualitative evaluation of results is done by amateurs and experts of this problematic. It is done by anonymously comparing this solution to another method of eliminating curtaining effect. Solution presents new and promising approach to elimination of curtaining effect and contributes to a better procedure of dealing with images which are created during material analysis.
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Monitor of Exploitation in Ultramicro Aviation
Kudera, Matěj ; Dobeš, Petr (referee) ; Zemčík, Pavel (advisor)
The aim of this bachelor's thesis was to create a system that will record the operation of an ultralight aircraft in which it will be installed. The thesis analyzes the principles important for the design of this system and creates a detailed proposal, which is based on the acquired knowledge of individual principles. The created system consists of two parts. An embedded device that is built into the ultralight aircraft and records whether it is in motion and a mobile application that allows easy access to records made by the embedded device. The mobile application was made for the Android operating system using the Android Studio development environment and the embedded device was implemented using a Raspberry Pi minicomputer, to which the necessary peripherals were connected. Finally, the functionality of the system was tested using the created tests and test flights of ultralight aircraft with embedded device were performed.
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Deep Neural Networks for Reinforcement Learning
Košák, Václav ; Dobeš, Petr (referee) ; Hradiš, Michal (advisor)
The paper describes a training environment for training a character how to walk. The environment is implemented in Al Gym by using the PyBullet physical model. Tasks from the environment are solved by using reinforcement learning by the ActorCritic algorithm. Each of the tasks is focused on the fundamental movements of the character. The paper show, which reward functions are used by the algorithm to solve given tasks.
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New Generation of Open-Source Tool Stranger Strings
Kňazík, Matej ; Dobeš, Petr (referee) ; Herout, Adam (advisor)
Cieľom tejto bakalárskej práce je opísať vývoj webovej aplikácie s názvom Stranger Strings. Projekt si ponechal svoje meno po internom firemnom nástroji, avšak vo všetkom ostatnom prešiel kompletnými zmenami. Účel Stranger Strings sa pozmenil, kód bol od základu prepísaný a celý projekt bol zmenený na open-source. Rovnako bolo redizajnované aj užívateľské prostredie za účelom rozšírenia cieľovej skupiny užívateľov. Táto práca podrobne popisuje tento proces a tiež vysvetľuje, akú úlohu zohralo užívateľské testovanie pri identifikácii hlavných problémov aplikácie. Výsledkom tejto práce je open-source nástroj na analýzu lokalizácie, ktorý pomáha užívateľom zlepšovať jej kvalitu.
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Mobile App - Journal as a Chat
Dorda, Tomáš ; Dobeš, Petr (referee) ; Herout, Adam (advisor)
This application aimed to create a minimalist mobile application for the secure keeping of an electronic diary with the user interface of the instant messaging application. The application is implemented in the Flutter framework and is available for devices with the Android operating system. The work focuses on the design of the application, its implementation, and continuous testing. The result is a journaling application that allows any journal to be locked with its own password, hidden, or even hidden and locked. The application offers a large number of color themes to customize each diary and an original user interface.
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