Publications by authors named "Emilie Neveu"
Article Synopsis
- Many intracellular pathogens, like bacteria and large viruses, use phagocytosis to enter eukaryotic cells and replicate without being degraded.
- Recent findings show that bacteria from the order Legionellales possess SNARE proteins, which help in vesicle trafficking, indicating they might manipulate cellular transport mechanisms.
- Giant viruses also have SNARE proteins and other trafficking factors, suggesting that they can utilize a diverse set of tools for interference with host cell processes, warranting further research on their role during viral infections.
Article Synopsis
- * In the study, researchers identified three unique nitric oxide synthase (NOS) genes in the placozoans Trichoplax and Hoilungia and confirmed their functional presence by measuring NO-related compounds using advanced techniques.
- * The findings reveal a more complex signaling system in placozoans than previously thought, with diverse NOSs and NO receptors that suggest significant evolutionary adaptations in their cellular mechanisms compared to more complex animals.
Article Synopsis
- Eukaryotic cells are characterized by various membrane-bound organelles that create distinct compartments, yet the origins of this internal complexity are not fully understood.
- Vesicle-mediated exchanges between organelles are crucial, with SNARE proteins playing a key role in the fusion process and being unique to eukaryotes.
- Researchers discovered SNARE-like proteins in Asgard archaea, suggesting a common ancestral lineage with eukaryotes, but the exact nature of their membrane systems remains to be investigated further.
Motivation: The root mean square deviation (RMSD) is one of the most used similarity criteria in structural biology and bioinformatics. Standard computation of the RMSD has a linear complexity with respect to the number of atoms in a molecule, making RMSD calculations time-consuming for the large-scale modeling applications, such as assessment of molecular docking predictions or clustering of spatially proximate molecular conformations. Previously, we introduced the RigidRMSD algorithm to compute the RMSD corresponding to the rigid-body motion of a molecule.
View Article and Find Full Text PDFMotivation: Docking prediction algorithms aim to find the native conformation of a complex of proteins from knowledge of their unbound structures. They rely on a combination of sampling and scoring methods, adapted to different scales. Polynomial Expansion of Protein Structures and Interactions for Docking (PEPSI-Dock) improves the accuracy of the first stage of the docking pipeline, which will sharpen up the final predictions.
View Article and Find Full Text PDFWe present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank.
View Article and Find Full Text PDFThe 2013-2014 CSAR docking exercise was the opportunity to assess the performance of the novel knowledge-based potential we are developing, named Convex-PL. The data used to derive the potential consists only of structural information from protein-ligand interfaces found in the PDBBind database. As expected, our potential proved to be very efficient in the near-native pose detection exercises, where we correctly predicted two near-native poses in the 2013 exercise and also ranked 22 near-native poses first and 2 second in the 2014 exercise.
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