DeepRank-GNN: A Graph Neural Network Framework to Learn Patterns in Protein-Protein Interfaces

MOTIVATION: Gaining structural insights into the protein-protein interactome is essential to understand biological phenomena and extract knowledge for rational drug design or protein engineering. We have previously developed DeepRank, a deep-learning framework to facilitate pattern learning from protein-protein interfaces using convolutional neural network (CNN) approaches. However, CNN is not rotation invariant and data augmentation is required to desensitize the network to the input data orientation which dramatically impairs the computation performance. Representing protein-protein complexes as atomic- or residue-scale rotation invariant graphs instead enables using graph neural networks (GNN) approaches, bypassing those limitations. RESULTS: We have developed DeepRank-GNN, a framework that converts protein-protein interfaces from PDB 3D coordinates files into graphs that are further provided to a pre-defined or user-defined GNN architecture to learn problem-specific interaction patterns. DeepRank-GNN is designed to be highly modularizable, easily customized and is wrapped into a user-friendly python3 package. Here, we showcase DeepRank-GNN's performance on two applications using a dedicated graph interaction neural network: (i) the scoring of docking poses and (ii) the discriminating of biological and crystal interfaces. In addition to the highly competitive performance obtained in those tasks as compared to state-of-the-art methods, we show a significant improvement in speed and storage requirement using DeepRank-GNN as compared to DeepRank. AVAILABILITY AND IMPLEMENTATION: DeepRank-GNN is freely available from https://github.com/DeepRank/DeepRank-GNN. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Electron Acceleration by Relativistic Surface Plasmons in Laser-Grating Interaction

The generation of energetic electron bunches by the interaction of a short, ultraintense (I>1019 W/cm2) laser pulse with "grating" targets has been investigated in a regime of ultrahigh pulse-to-prepulse contrast (1012). For incidence angles close to the resonant condition for surface plasmon excitation, a strong electron emission was observed within a narrow cone along the target surface, with energy spectra peaking at 5-8 MeV and total charge of ∼100 pC. Both the energy and the number of emitted electrons were strongly enhanced with respect to simple flat targets. The experimental data are closely reproduced by three-dimensional particle-in-cell simulations, which provide evidence for the generation of relativistic surface plasmons and for their role in driving the acceleration process. Besides the possible applications of the scheme as a compact, ultrashort source of MeV electrons, these results are a step forward in the development of high-field plasmonics

Benzofuran-fused Phosphole: Synthesis, Electronic, and Electroluminescence Properties

International audienceA synthetic route to novel benzofuran-fused phosphole derivatives 3-5 is described. These compounds showed optical and electrochemical properties that differ from their benzothiophene analog. Preliminary results show that 4 can be used as an emitter in OLEDs, illustrating the potential of these new compounds for opto-electronic applications

Etude des propriétés conductrices des phases Na2Mg2Ti6O14F2 alpha et beta

International audienceLa conductivité des ions sodium au sein des variétés alpha et beta de Na2Mg2Ti6O14F2 a été étudiée par la méthode des impédances complexes..

Processus de clustérization au sein des solutions solides Ca1−xLnx F2+x (Ln=La, Nd, Gd) comportant un substituant trivalent lanthanidique de grande taille

International audienc

Influence of the fluorine-oxygen substitution on the ionic conductivity properties of lithium tellurite glasses

A large range of glassy compositions has been found inside the ternary LiF-Li2O-TeO2 system. The influence of the fluorine-oxygen substitution on the ionic conduction properties of (50-x)LiO0.5-(x)LiF-(50)TeO2 ([MATH]) glasses has been investigated. These results have been correlated with the data relative to ion distribution and microstructure obtained by NMR and TEM. A maximum of conductivity associated with a minimum of activation energy is observed for [MATH]. The composition dependence of conductivity with rising x can be explained by a progressive decrease of the F-F associations around the Te4+ ions and a simultaneous increase of the Li-F associations. The clustering of the Li+ and F- ions produces small domains which hinder the Li+ ions diffusion in these glasses

Binding energies of first and second shell water molecules in the Fe(H

The fragmentation cross-section of the Fe(H2O)$_{1,2}^+$, Co(H2O)$_{1,2}^+$ and Au(H2O)$_{1,2}^+$ ions were measured, as a function of the collision energy. Threshold energies of $1.4\pm0.2$ eV, $1.4\pm0.2$ eVand $1.7\pm0.1$ eVwere measured for the monohydrated $\rm Fe^+$, $\rm Co^+$ and $\rm Au^+$ ions respectively, in fair agreement with the existing literature. Small threshold energies of $0.7\pm0.2$ eV, $0.7\pm0.2$ eVand $0.5\pm0.1$ eV were found for the Fe(H2O)$_{2}^+$, Co(H2O)$_{2}^+$ and Au(H2O)$_{2}^+$ clusters respectively. Secondary thresholds were observed on the cross-section, respectively at $1.7\pm0.3$ eV and $2.0\pm0.2$ eV for the Co(H2O)$_{2}^+$ and Au(H2O)$_{2}^+$ clusters. This double threshold behavior could be attributed to the presence of two kinds of isomers in the beam. The upper threshold is associated with clusters where both water molecules are linked to the metal ion (first solvation shell), whereas the lower threshold corresponds to clusters with one water molecule in the first solvation shell and the other in the second shell. Such an analysis documents the binding energy of either a first shell or a second shell water molecule in the M(H2O)$_{2}^+$ cluster ions

La nacre Pinctada margaritifera : caractérisation physico-chimique, propriétés biomécaniques et cytocompatibilité in vitro

Pinctada maxima nacra (mother-of-pearl) has been recently proposed as a bone substitute. The purpose of this work was to assess the in vitro cytocompatibility of Pinctada margaritifera nacre and its physico-chemical and biomechanical properties