PMG: online generation of high-quality molecular pictures and storyboarded animations

The Protein Movie Generator (PMG) is an online service able to generate high-quality pictures and animations for which one can then define simple storyboards. The PMG can therefore efficiently illustrate concepts such as molecular motion or formation/dissociation of complexes. Emphasis is put on the simplicity of animation generation. Rendering is achieved using Dino coupled to POV-Ray. In order to produce highly informative images, the PMG includes capabilities of using different molecular representations at the same time to highlight particular molecular features. Moreover, sophisticated rendering concepts including scene definition, as well as modeling light and materials are available. The PMG accepts Protein Data Bank (PDB) files as input, which may include series of models or molecular dynamics trajectories and produces images or movies under various formats. PMG can be accessed at http://bioserv.rpbs.jussieu.fr/PMG.html

In Silico Studies on DARC.

International audienceThe Duffy Antigen/Receptor for Chemokine (DARC) is a seven segment transmembrane protein. It was firstly discovered as a blood group antigen and was the first specific gene locus assigned to a specific autosome in man. It became more famous as an erythrocyte receptor for malaria parasites (Plasmodium vivax and Plasmodium knowlesi), and finally for chemokines. DARC is an unorthodox chemokine receptor as (i) it binds chemokines of both CC and CXC classes and (ii) it lacks the Asp-Arg-Tyr consensus motif in its second cytoplasmic loop hence cannot couple to G proteins and activate their signaling pathways. DARC had also been associated to cancer progression, numerous inflammatory diseases, and possibly to AIDS. In this review, we will summarize important biological data on DARC. Then we shall focus on recent development of the elaboration and analyzes of structural models of DARC. We underline the difficulty to propose pertinent structural models of transmembrane protein using comparative modeling process, and other dedicated approaches as the Protein Blocks. The chosen structural models encompass most of the biochemical data known to date. Finally, we present recent development of protein - protein docking between DARC structural models and CXCL-8 structures. We propose a hierarchal search based on separated rigid and flexible docking

Advances in Human-Protein Interaction - Interactive and Immersive Molecular Simulations

International audienc

Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics

Coarse-grained models have long been considered indispensable tools in the investigation of biomolecular dynamics and assembly. However, the process of simulating such models is arduous because unconventional force fields and particle attributes are often needed, and some systems are not in thermal equilibrium. Although modern molecular dynamics programs are highly adaptable, software designed for preparing all-atom simulations typically makes restrictive assumptions about the nature of the particles and the forces acting on them. Consequently, the use of coarse-grained models has remained challenging. Moltemplate is a file format for storing coarse-grained molecular models and the forces that act on them, as well as a program that converts moltemplate files into input files for LAMMPS, a popular molecular dynamics engine. Moltemplate has broad scope and an emphasis on generality. It accommodates new kinds of forces as they are developed for LAMMPS, making moltemplate a popular tool with thousands of users in computational chemistry, materials science, and structural biology. To demonstrate its wide functionality, we provide examples of using moltemplate to prepare simulations of fluids using many-body forces, coarse-grained organic semiconductors, and the motor-driven supercoiling and condensation of an entire bacterial chromosome

Analyse des systèmes tenase et prothrombinase par bioinformatique structurale (prédiction de complexes macromoléculaires et proposition d'agents anti-coagulants)

Analyse des systèmes tenase et prothrombinase par bioinformatique structurale : prédiction de complexes macromoléculaires et proposition d'agents anticoagulants. Les deux complexes protéiques Tenase (F8a, F9a, F10) et Prothrombinase (F5a, F10a, PTH), sont les éléments pivots de la coagulation du sang. Ces complexes reposent sur des interactions protéineprotéine dont la nature moléculaire reste peu connue. La bioinformatique va nous permettre de mieux comprendre ces interactions. Une des méthodes prometteuses en découlant est le " docking " : étant données les coordonnées atomiques de deux molécules, il faut prédire le mode de liaison "correcte". Cette approche par docking nous a permis de générer des milliers de complexes. Par le biais de filtres successifs, utilisant des données expérimentales, nous avons sélectionné 10 complexes du tenase différents et un modèle du prothrombinase tous en accord avec les données expérientales. Ces modèles ouvrent la porte à des expérimentations clarifiant certains points ambigus, et à des études de criblage virtuel afin d'identifier de nouvaux agents potentiellement actives à l'interface protéineprotéin.PARIS-BIUP (751062107) / SudocSudocFranceF

Integrative modeling of JCVI-Syn3A nucleoids with a modular approach

A lattice-based method is presented for creating 3D models of entire bacterial nucleoids integrating ultrastructural information cryoelectron tomography, genomic and proteomic data, and experimental atomic structures of biomolecules and assemblies. The method is used to generate models of the minimal genome bacterium JCVI-Syn3A, producing a series of models that test hypotheses about transcription, condensation, and overall distribution of the genome. Lattice models are also used to generate atomic models of an entire JCVI-Syn3A cell

Integrative Modeling and Visualization of Exosomes

Information from proteomics, microscopy, and structural biology are integrated to create structural models of exosomes, small vesicles released from cells. Three visualization methods are employed and compared: 2D painting of a cross section using traditional media, manual creation of a cross section using the mesoscale 2.5D digital painting software cellPAINT, and generation of a 3D atomic model using the mesoscale modeling program cellPACK