Search results for "Structural Biology."
showing 10 items of 822 documents
UVPAR: fast detection of functional shifts in duplicate genes.
2006
Abstract Background The imprint of natural selection on gene sequences is often difficult to detect. A plethora of methods have been devised to detect genetic changes due to selective processes. However, many of those methods depend heavily on underlying assumptions regarding the mode of change of DNA sequences and often require sophisticated mathematical treatments that made them computationally slow. The development of fast and effective methods to detect modifications in the selective constraints of genes is therefore of great interest. Results We describe UVPAR, a program designed to quickly test for changes in the functional constraints of duplicate genes. Starting with alignments of t…
Transglutaminase and polyamine dependence of effector functions of human immunocompetent cells
1982
AbstractThe effects of the transglutaminase inhibitor dansyl cadaverine (DC) and the polyamine antagonist methyl glyoxal-bis-(guanylhydrazone) (MeGbG) on the response of lymphocytes towards allogeneic and lectin stimulation and on the zymosan-induced chemiluminescence of neutrophilic granulocytes was studied. Application of DC resulted in dose-dependent suppression of chemiluminiscence and lymphocyte proliferation; no difference of inhibitory potential occurred with variation of incubation time in the latter system. MeGbG was inactive in granulocytes, but inhibited lymphocyte proliferation; its effect increased with time. The experiments provide further evidence for the importance of transg…
Analyzing big datasets of genomic sequences: fast and scalable collection of k-mer statistics
2019
Abstract Background Distributed approaches based on the MapReduce programming paradigm have started to be proposed in the Bioinformatics domain, due to the large amount of data produced by the next-generation sequencing techniques. However, the use of MapReduce and related Big Data technologies and frameworks (e.g., Apache Hadoop and Spark) does not necessarily produce satisfactory results, in terms of both efficiency and effectiveness. We discuss how the development of distributed and Big Data management technologies has affected the analysis of large datasets of biological sequences. Moreover, we show how the choice of different parameter configurations and the careful engineering of the …
PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources.
2019
Background Biological databases and repositories are incrementing in diversity and complexity over the years. This rapid expansion of current and new sources of biological knowledge raises serious problems of data accessibility and integration. To handle the growing necessity of unification, CellBase was created as an integrative solution. CellBase provides a centralized NoSQL database containing biological information from different and heterogeneous sources. Access to this information is done through a RESTful web service API, which provides an efficient interface to the data. Results In this work we present PyCellBase, a Python package that provides programmatic access to the rich RESTfu…
Principal component analysis on molecular descriptors as an alternative point of view in the search of new Hsp90 inhibitors
2009
Inhibiting a protein that regulates multiple signal transduction pathways in cancer cells is an attractive goal for cancer therapy. Heat shock protein 90 (Hsp90) is one of the most promising molecular targets for such an approach. In fact, Hsp90 is a ubiquitous molecular chaperone protein that is involved in folding, activating and assembling of many key mediators of signal transduction, cellular growth, differentiation, stress-response and apoptothic pathways. With the aim to analyze which molecular descriptors have the higher importance in the binding interactions of these classes, we first performed molecular docking experiments on the 187 Hsp90 inhibitors included in the BindingDB, a pu…
A knowledge-based decision support system in bioinformatics: An application to protein complex extraction
2013
Abstract Background We introduce a Knowledge-based Decision Support System (KDSS) in order to face the Protein Complex Extraction issue. Using a Knowledge Base (KB) coding the expertise about the proposed scenario, our KDSS is able to suggest both strategies and tools, according to the features of input dataset. Our system provides a navigable workflow for the current experiment and furthermore it offers support in the configuration and running of every processing component of that workflow. This last feature makes our system a crossover between classical DSS and Workflow Management Systems. Results We briefly present the KDSS' architecture and basic concepts used in the design of the knowl…
Induction of tcI 7 , a gene encoding a β-subunit of proteasome, in tobacco plants treated with elicitins, salicylic acid or hydrogen peroxide 1
2000
We previously isolated, by differential display and 5′ RACE (rapid amplification of cDNA ends), cDNAs corresponding to genes activated following cryptogein treatment of tobacco cell suspensions, among them tcI 7 (tcI for obacco ryptogein nduced), a gene encoding a β-subunit of proteasome. Here, we report that tcI 7 was up-regulated in tobacco plants treated with elicitins (cryptogein and parasiticein) that have been shown to induce a systemic acquired resistance (SAR). Moreover, subsequent inoculation of tobacco with the pathogen Phytophthora parasitica var. nicotianae (Ppn) was shown to induce an additional activation of tcI 7 in tobacco plants pretreated with cryptogein. We also showed an…
Anisotropic lattice distortions in biogenic calcite induced by intra-crystalline organic molecules.
2006
9 pages; International audience; We have performed precise structural measurements on five different calcitic seashells by high-resolution X-ray powder diffraction on a synchrotron beam line and by laboratory single crystal X-ray diffraction. The unit cell parameters a and c of biogenic calcite were found to be systematically larger than those measured in the non-biogenic calcite. The maximum lattice distortion (about 2.10(-3)) was detected along the c-axis. Under heat treatment above 200 degrees C, a pronounced lattice relaxation was observed, which allowed us to conclude that anisotropic lattice swelling in biogenic calcite is induced by organic macromolecules incorporated within the sing…
Application of clustering techniques to electron-diffraction data: determination of unit-cell parameters.
2012
A new approach to determining the unit-cell vectors from single-crystal diffraction data based on clustering analysis is proposed. The method uses the density-based clustering algorithm DBSCAN. Unit-cell determination through the clustering procedure is particularly useful for limited tilt sequences and noisy data, and therefore is optimal for single-crystal electron-diffraction automated diffraction tomography (ADT) data. The unit-cell determination of various materials from ADT data as well as single-crystal X-ray data is demonstrated.
On the application of an experimental multipolar pseudo-atom library for accurate refinement of small-molecule and protein crystal structures
2007
International audience; With an increasing number of biomacromolecular crystal structures being measured to ultra-high resolution, it has become possible to extend to large systems experimental charge-density methods that are usually applied to small molecules. A library has been built of average multipole populations describing the electron density of chemical groups in all 20 amino acids found in proteins. The library uses the Hansen & Coppens multipolar pseudo-atom model to derive molecular electron density and electrostatic potential distributions. The library values are obtained from several small peptide or amino acid crystal structures refined against ultra-high-resolution X-ray diff…