Search results for "Databases"
showing 10 items of 937 documents
Efficient virtual screening using multiple protein conformations described as negative images of the ligand-binding site.
2010
The protein structure-based virtual screening is typically accomplished using a molecular docking procedure. However, docking is a fairly slow process that is limited by the available scoring functions that cannot reliably distinguish between active and inactive ligands. In contrast, the ligand-based screening methods that are based on shape similarity identify the active ligands with high accuracy. Here, we show that the usage of negative images of the ligand-binding site, together with shape comparison tools, which are typically used in ligand-based virtual screening, improve the discrimination of active molecules from inactives. In contrast to ligand-based shape comparison, the negative …
Protein knot server: detection of knots in protein structures
2007
KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regul…
NightShift: NMR shift inference by general hybrid model training--a framework for NMR chemical shift prediction.
2012
Background NMR chemical shift prediction plays an important role in various applications in computational biology. Among others, structure determination, structure optimization, and the scoring of docking results can profit from efficient and accurate chemical shift estimation from a three-dimensional model. A variety of NMR chemical shift prediction approaches have been presented in the past, but nearly all of these rely on laborious manual data set preparation and the training itself is not automatized, making retraining the model, e.g., if new data is made available, or testing new models a time-consuming manual chore. Results In this work, we present the framework NightShift (NMR Shift …
Une nouvelle approche mixte d'enrichissement de dimensions dans un schéma multidimensionnel en constellation Application à la biodiversité des oiseaux
2015
International audience; Les entrepôts de données (DW) et les systèmes OLAP sont des technologies d'analyse en ligne pour de grands volumes de données, basés sur les be-soins des utilisateurs. Leur succès dépend essentiellement de la phase de conception où les exigences fonctionnelles sont confrontées aux sources de données (méthodologie de conception mixte). Cependant, les méthodes de conception existantes semblent parfois inefficaces, lorsque les décideurs définissent des exi-gences fonctionnelles qui ne peuvent être déduites à partir des sources de don-nées (approche centrée sur les données), ou lorsque le décideur n'a pas intégré tous ces besoins durant la phase de conception (approche c…
On Generalizing Lipschitz Global Methods forMultiobjective Optimization
2015
Lipschitz global methods for single-objective optimization can represent the optimal solutions with desired accuracy. In this paper, we highlight some directions on how the Lipschitz global methods can be extended as faithfully as possible to multiobjective optimization problems. In particular, we present a multiobjective version of the Pijavskiǐ-Schubert algorithm.
Halloysite Nanotube with Fluorinated Lumen: Non-Foaming Nanocontainer for Storage and Controlled Release of Oxygen in Aqueous Media
2014
Halloysite clay nanotubes were selectivity modified by adsorbing perfluoroalkylated anionic surfactants at the inner surface. The modified nanotubes formed kinetically stable dispersions due to the enhanced electrostatic repulsions exercised between the particles. We proved that the modified nanotubes can be used as non-foaming oxygen nanocontainers in aqueous media. The gas release from supersaturated dispersions can be controlled by external stimuli and system composition. In conclusion, we managed to put forward an easy strategy to develop smart materials from natural nanoclays, which can endow important applications like the storage and delivery of gas.
Discordance between two national health statistics sources (EMH and EESCRI, 1990–2009). Analysis of psychiatric morbidity
2013
Abstract Introduction Two statistical sources provide data on hospital stays and discharges for all Spanish hospitals: Hospital Morbidity Survey (acronym in Spanish: EMH) and Statistics of Health Establishments providing Inpatient Care (acronym in Spanish: EESCRI). Our aim is to contrast these two statistical sources to define their accuracy and relevance in psychiatric epidemiology studies. Material and methodology The analysis is based on two aspects: (1) Compare the number of psychiatric stays and hospital discharges from 1990 to 2009. (2) Analyse and compare how the average stay is provided. Results The differences between the two statistical sources are significant and increase over ti…
Enhancing Privacy and Authorization Control Scalability in the Grid through Ontologies
2009
The use of data Grids for sharing relevant data has proven to be successful in many research disciplines. However, the use of these environments when personal data are involved (such as in health) is reduced due to its lack of trust. There are many approaches that provide encrypted storages and key shares to prevent the access from unauthorized users. However, these approaches are additional layers that should be managed along with the authorization policies. We present in this paper a privacy-enhancing technique that uses encryption and relates to the structure of the data and their organizations, providing a natural way to propagate authorization and also a framework that fits with many u…
Hints from the Crowd: A Novel NoSQL Database
2013
The crowd can be an incredible source of information. In particular, this is true for reviews about products of any kind, freely provided by customers through specialized web sites. In other words, they are social knowledge, that can be exploited by other customers. The Hints From the Crowd HFC prototype, presented in this paper, is a NoSQL database system for large collections of product reviews; the database is queried by expressing a natural language sentence; the result is a list of products ranked based on the relevance of reviews w.r.t. the natural language sentence. The best ranked products in the result list can be seen as the best hints for the user based on crowd opinions the revi…
Biologically based models of cancer risk in radiation research
2020
PURPOSE: In radiation risk analysis the state-of-the-art approach is based on descriptive models which link excess rates of cancer incidence and mortality to radiation exposure by statistical association. To estimate the number of sporadic and radiation-induced cases descriptive models apply parametric dose response function which directly determine the radiation risk. In biologically-based models of cancer risk (BBCR models) dose responses are implemented for key events on the biological level such as early mutations or clonal expansion of initiated cells. Influenced by radiation these events then shape the risk response on the epidemiological level. Although BBCR models facilitate a more …