Shape: automatic conformation prediction of carbohydrates using a genetic algorithm

<p>Abstract</p> <p>Background</p> <p>Detailed experimental three dimensional structures of carbohydrates are often difficult to acquire. Molecular modelling and computational conformation prediction are therefore commonly used tools for three dimensional structure studies. Modelling procedures generally require significant training and computing resources, which is often impractical for most experimental chemists and biologists. <monospace>Shape</monospace> has been developed to improve the availability of modelling in this field.</p> <p>Results</p> <p>The <monospace>Shape</monospace> software package has been developed for simplicity of use and conformation prediction performance. A trivial user interface coupled to an efficient genetic algorithm conformation search makes it a powerful tool for automated modelling. Carbohydrates up to a few hundred atoms in size can be investigated on common computer hardware. It has been shown to perform well for the prediction of over four hundred bioactive oligosaccharides, as well as compare favourably with previously published studies on carbohydrate conformation prediction.</p> <p>Conclusion</p> <p>The <monospace>Shape</monospace> fully automated conformation prediction can be used by scientists who lack significant modelling training, and performs well on computing hardware such as laptops and desktops. It can also be deployed on computer clusters for increased capacity. The prediction accuracy under the default settings is good, as it agrees well with experimental data and previously published conformation prediction studies. This software is available both as open source and under commercial licenses.</p

L’explicitation de l’utilisation de l’estimation permet-elle d’améliorer les performances des élèves en calcul et en résolution de problèmes ?

Few studies have been conducted on estimation learning in arithmetics, on its influence on calculation and on problem solving. To our knowledge, no study has been carried out on direct instruction in estimation in mathematics. In this context, we were wondering if the explicitness in the instruction of the estimated result calculation can improve children performance in estimated calculation, in exact calculation and in problem solving. Our study was conducted on three classes (CM1, CM2 and CM1-CM2), and followed three steps: a training phase, a pre-test phase and an experimental phase. For the final phase, children were divides into two groups: an experimental group for which the explicitness of using the estimation before calculating the exact result was required and a control group for which the estimation was not explicitly required. Results don’t show any effect of the explicitness of using estimated results in the instruction on children’s performance in estimated calculation, in exact calculation and in problem resolution. However, a correlation was observed between children’s performance in estimated calculation and their performance in exact calculation and in problem solving.Peu d’études ont été faites sur l'apprentissage de l’estimation en calcul et sur son influence sur les résultats en calcul et en résolution de problèmes. A notre connaissance, aucune étude n’a été faite sur l'enseignement explicite de l'estimation. C'est dans ce cadre que nous nous sommes interrogées afin de savoir si l’explicitation du calcul d’un résultat estimé dans la consigne permet d’augmenter les performances des élèves en calcul estimé, en calcul exact et en résolution de problème. Pour notre étude, menée sur trois classes (CM1, CM2 et CM1-CM2), nous avons choisi de fonctionner en trois phases, une phase d'entraînement, un pré-test et une phase expérience. Pour cette dernière, nos élèves ont été répartis en deux groupes : un groupe expérience, qui a eu la consigne explicite d’estimer les résultats avant de réaliser le calcul exact puis, un groupe contrôle, qui n'a pas reçu cette consigne. Les résultats obtenus ne montrent pas d'effet de l’explicitation du calcul d’un résultat estimé dans la consigne sur les performances des élèves en calcul estimé, en calcul exact et en résolution de problèmes. Cependant, une corrélation a été observée entre la performance des élèves en calcul estimé, en calcul exact et en résolution de problème

TGV nouvelle generation

Available from INIST (FR), Document Supply Service, under shelf-number : RL 390 (1); RL 390 (2) / INIST-CNRS - Institut de l'Information Scientifique et TechniqueSIGLEMinistere de l'Equipement, des Transports et du Logement (METL), 92 - Puteaux (France). Direction de la Recherche et des Affaires Scientifiques et Techniques (DRAST)FRFranc

Discovery of New Inhibitors of Resistant Streptococcus pneumoniae Penicillin Binding Protein (PBP) 2x by Structure-Based Virtual Screening.

Penicillin binding proteins (PBPs) are involved in the biosynthesis of the peptidoglycan layer constitutive of the bacterial envelope. They have been targeted for more than half a century by extensively derived molecular scaffolds of penicillins and cephalosporins. Streptococcus pneumoniae resists the antibiotic pressure by inducing highly mutated PBPs that can no longer bind the beta-lactam containing agents. To find inhibitors of PBP2x from Streptococcus pneumoniae (spPBP2x) with novel chemical scaffold so as to circumvent the resistance problems, a hierarchical virtual screening procedure was performed on the NCI database containing approximately 260000 compounds. The calculations involved ligand-based pharmacophore mapping studies and molecular docking simulations in a homology model of spPBP2x from the highly resistant strain 5204. A total of 160 hits were found, and 55 were available for experimental tests. Three compounds harboring two novel chemical scaffolds were identified as inhibitors of the resistant strain 5204-spPBP2x at the micromolar range.EUR-INTAFA

Mutations in the ERCC2 (XPD) gene associated with severe fetal ichthyosis and dysmorphic features

International audienceCongenital ichthyosis is a condition that includes several distinct subtypes with significant genetic heterogeneity. Defects in the ERCC2 [xeroderma pigmentosum (XP) complementation group D] gene lead to one of several clinical diseases, including XP, trichothiodystrophy, cerebrooculofacioskeletal syndrome, XP/Cockayne syndrome, and XP/trichothiodystrophy

Cholangite aiguë après prise d’ibuprofène

International audienceAlveolar echinococcosi. Alveolar echinococcosis is a parasitic anthropo-zoonosis which looks like a slow-growing liver cancer. The lesions progressively obstruct hepatic vessels and bile ducts and invade neighboring organs, and it may metastasize to the lung and the brain and possibly all distant organs. Since the 1990s earlier diagnosis by imaging, advances in surgical and less invasive interventions, and prolonged anti-parasitic treatment using albendazole, have totally transformed the prognosis of the disease. However, in Europe, the endemic area has considerably increased, the number of alveolar echinococcosis cases has more than doubled in the previously identified endemic regions, and the disease may now be considered to be an 'opportunistic infection', especially diagnosed in those patients treated with immunosuppressive drugs and biologic agents. Alveolar echinococcosis is currently more and more often diagnosed incidentally, at an early stage of development, and not in the usual 'at risk' regions and populations. This makes differential diagnosis and care management more challenging

High Affinity Interaction between a Bivalve C-type Lectin and a Biantennary Complex-type N -Glycan Revealed by Crystallography and Microcalorimetry

International audienc