CABS-flex predictions of protein flexibility compared with NMR ensembles

Motivation: Identification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles. Results: Based on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting of protein regions that undergo conformational changes and the extent of such changes

Gaze Detection using Facial Landmarks

Import 03/11/2016Tématem této diplomové práce je detekce úhlu pohledu za využití významných bodů obličeje. Vytvořený program využívá již hotové implementace detektoru významných bodů, pomocí kterého jsou nalezeny oční oblasti. Tyto oblasti jsou využity k detekci obvodu a středu duhovky pomocí Houghovy transformace. Střed duhovky je dále poměřován s oční oblastí a na základě jeho polohy je vyhodnocen úhel pohledu pozorované osoby. Z důvodu odstranění mírné nestability detekce úhlu pohledu, způsobené detektorem významných bodů, obsahuje detektor paměť předchozích detekcí, které aproximují detekci aktuálního snímku. Teoretická část je zaměřena na uplatnění a popis konkrétních řešení detektoru významných bodů obličeje a detektoru duhovek a zornic. Praktická část popisuje samotný algoritmus detekce úhlu pohledu a testy, které na něm byly provedeny.The subject of this master thesis was a gaze detection using facial landmarks. The created program uses already finished implementation of facial landmarks detector. This detector is used to find eye regions. Using these regions the circuit and the center of iris is detected by Hough transform. Based on the position of iris center, inside the eye region, the person's eye gaze is calculated. A buffer which stores a specific number of detections is used. These past detections help to approximate the current image detection. The theoretical part is focused on motivation and description of a specific solutions of facial landmarks detector and iris and pupil detector. The practical part describes the created eye gaze detection algorithm itself and the performed tests.460 - Katedra informatikyvýborn

IP Camera Security System with Web Interface

Import 05/08/2014Po přečtení této práce by měl čtenář získat základní orientaci v tématech zabývajících se IP kamerami, softwarem kamerových systémů a standardizací výroby kamerových zařízení. První část rozebírající problematiku IP kamer poskytuje seznámení s jednotlivými hardwarovými součástmi, funkcemi a obrazovými vlastnostmi kamer. Ve druhé části se čtenář má možnost seznámit s kamerovými systémy. Především jsou zde srovnána jednotlivá zařízení umožňující centralizovanou správu kamer a shromažďování obrazových dat. V další kapitole je popsán standard ONVIF, který poskytuje poměrně jednoznačná pravidla dnes již značně rozšířené skupině společností zabývajících se výrobou kamerových zařízení. V poslední části je popsán vývoj vlastního kamerového systému počínaje analýzou systému, přes popis použitých technologií, až po samotnou implementaci systému.After reading this paper the reader should gain basic knowledge of issues dealing with IP cameras, CCTV systems and standardizing the production of camera equipment. The first part is discussing the issue of IP cameras. It provides an introduction to the various hardware components, functions and optical properties of cameras. In the second part, the reader has the opportunity to become familiar with the camera systems. There are primarily compared various devices enabling centralized management of cameras and collecting visual data. The next chapter describes the ONVIF standard, which provides a relatively clear rules to group of involved companies engaged in the production of camera equipment. The last part describes the development of a custom camera system software, starting with analysis of the system, through the description of used technologies, till the project system implementation.460 - Katedra informatikyvýborn

KnotProt: a database of proteins with knots and slipknots

The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprint

AGGRESCAN3D (A3D) : server for prediction of aggregation properties of protein structures

Altres ajuts: ICREA Academia 2009 to S.VProtein aggregation underlies an increasing number of disorders and constitutes a major bottleneck in the development of therapeutic proteins. Our present understanding on the molecular determinants of protein aggregation has crystalized in a series of predictive algorithms to identify aggregation-prone sites. A majority of these methods rely only on sequence. Therefore, they find difficulties to predict the aggregation properties of folded globular proteins, where aggregation-prone sites are often not contiguous in sequence or buried inside the native structure. The AGGRESCAN3D (A3D) server overcomes these limitations by taking into account the protein structure and the experimental aggregation propensity scale from the well-established AGGRESCAN method. Using the A3D server, the identified aggregation-prone residues can be virtually mutated to design variants with increased solubility, or to test the impact of pathogenic mutations. Additionally, A3D server enables to take into account the dynamic fluctuations of protein structure in solution, which may influence aggregation propensity. This is possible in A3D Dynamic Mode that exploits the CABS-flex approach for the fast simulations of flexibility of globular proteins. The A3D server can be accessed at http://biocomp.chem.uw.edu.pl/A3D/

Perspectives of deliberative poll as an innovation in health policy

The aim of this paper is a systematic description and classification of the deliberative poll (DP) as a potentially innovative method of participation in health policy. The paper discusses the theory of deliberative democracy and a specific method of deliberative polling, as well as examples of its application, along with critical commentary. It summarises the characteristics of DP: advantages and disadvantages, as well as conditions for proper application. In this context an important distinc tion is made between two ideal types of participation: co-decision and consultation. A key feature of the latter is its advisory, and not decisive, character. DP is considered an example of such non-decisive, consultative participation