Laboratoire de Biochimie Théorique
Présentation
The Laboratory of Theoretical Biochemistry (LBT) is one of five laboratories within Institut de Biologie Physico-Chimique (IBPC) in Paris.
LBT belongs to the French national research agency CNRS through its Institute of Chemistry, and is associated with Paris Diderot University. The laboratory was created at IBPC in 1958 as Laboratoire de Biochimie Théorique. Our field is theoretical and computational biochemistry, at the interface between biology, chemistry, physics, and computing.
Our strategic objectives are twofold: invent simulation algorithms to reproduce and predict physical properties of biomolecules either in vitro or in the cell, and understand the molecular or conformational factors responsible for the biological functions of living systems, and diseases. The equilibrium between these two aspects is the key point of the laboratory policy.
LBT is organized as a team of independent researchers with complementary interests and domains of expertise, both in method development and in biophysical, biochemical, and biomedical applications. Advances in each of these domains emerge from the association of different sets of researchers around individual projects.
Thèmes de recherche
Les axes de recherches du LBT se concentrent sur les développements méthodologiques et algorithmiques pour l’étude de la structure, la dynamique, la mécanique et les interactions des macromolécules biologiques.
Les objectifs sont donc d'utiliser les ordinateurs pour ouvrir des fenêtres vers le monde moléculaire, en aidant à comprendre les facteurs qui sous-tendent des faits expérimentaux, et en prédisant les propriétés et le comportement des molécules biologiques.
Equipes de recherche
Directeur : Marc Baaden
[hal-03184037] Tetrameric Abeta40 and Abeta42 beta-Barrel Structures by Extensive Atomistic Simulations. I. In a Bilayer Mimicking a Neuronal Membrane
Date: 29 Mar 2021 - 11:55
Desc: The amyloid-beta (Abeta) 42 oligomers are much more toxic than Abeta40 oligomers in Alzheimer's disease. Numerous experiments indicate that toxicity could involve the formation of pores in membranes, but experimental high-resolution structure determination of these pore-forming Abeta oligomers has been impeded by aggregate heterogeneity. Using extensive atomistic simulations, low-resolution data obtained in lipid bilayers, and other theoretical factors, we proposed atomic structures of Abeta40 and Abeta42 beta-barrels in a bilayer mimicking a neuronal membrane. The 3D model, which consists of tetramer subunits, two distinct beta-hairpin motifs and an asymmetric arrangement of eight antiparallel beta-strands, is drastically destabilized for Abeta40 compared to its Abeta42 counterpart. Our computational modeling has several implications in Alzheimer's disease, sheds light on the amyloid pore hypothesis, and explains the higher deleterious property of Abeta42.
[hal-01722019] Meet-U: educating through research immersion
Date: 3 Oct 2018 - 16:03
Desc: We present a new educational initiative, called Meet-U, that aims at training students to collaborativework in computational biology and at bridging the gap between education and research.Meet-U mimics the set up of collaborative research projects and takes advantage of the most populartools for collaborative work and of cloud computing. Students are grouped in teams of 4-5 peopleand have to realize a project from A to Z that answers a challenging question in Biology.Meet-U promotes "coopetition", as the students collaborate within and across the teams and are also incompetition with each other to develop the best final product.Meet-U fosters interactions between different actors of education and research through the organization of a meeting day, open to everyone, where the students present their work to a jury of researchers and jury members give researchseminars. This very unique combination of education and research is strongly motivating for thestudents and provides a formidable opportunity for a scientific community to unite and increase itsvisibility. We report on our experience with Meet-U in two French universities with master studentsin bioinformatics and modeling, with protein-protein docking as the subject of the course.Meet-U is easy to implement, virtually costs nothing and can be straightforwardly transferred to other fieldsand/or universities. All the information and data are available at http://www.meet-u.org.
[hal-01400465] Visualization of Biomolecular Structures: State of the Art Revisited
Date: 13 Ene 2023 - 14:05
Desc: Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The survey concludes with an outlook on promising and important research topics to foster further success in the development of tools that help to reveal molecular secrets.
[halshs-02424173] Itinéraires Bis
Date: 26 Dic 2019 - 18:47
Desc: Les chercheurs font rarement la une des journaux : l'annonce des prix Nobel, de rares manifestations, les polémiques de quelques grandes figures médiatiques, la réponse ciblée à une inquiétude suite à un phénomène de société, à cela se résume le plus souvent leur présence sur la scène médiatique. Que signifie être chercheur dans un contexte sociétal mouvant ? Quels sont les plaisirs et les difficultés de ce métier en pleine évolution ? En quoi consiste-t-il ? Comment et pourquoi devient-on chercheur ? Ce livre soulève ces quelques questions par le biais de témoignages de chercheurs d'horizons très divers, récemment recrutés au Centre National de la Recherche Scientifique (CNRS). L'initiative de ce livre est née à la suite de journées d'études axées sur les potentialités des itinéraires professionnels des chercheurs. Celles-ci ont mis en évidence de nombreux points communs malgré la diversité des parcours de « jeunes chercheurs » : des ressentis, des questions, des constats similaires, appuyés pourtant sur des expériences différentes. Les treize auteurs évoquent, au travers de leurs témoignages, toujours passionnés, parfois drôles, souvent émouvants, leurs « itinéraires » de chercheurs.
[hal-01084652] Interactive Molecular Dynamics: Scaling up to Large Systems
Date: 19 Nov 2014 - 17:02
Desc: Combining molecular dynamics simulations with user interaction would have various applications in both education and research. By enabling interactivity the scientist will be able to visualize the experiment in real time and drive the simulation to a desired state more easily. However, interacting with systems of interesting size requires significant computing resources due to the complexity of the simulation. In this paper, we propose an approach to combine a classical parallel molecular dynamics simulator, Gromacs, to a 3D virtual reality environment allowing to steer the simulation through external user forces applied with an haptic device to a selection of atoms. We specifically focused on minimizing the intrusion in the simulator code, on efficient parallel data extraction and filtering to transfer only the necessary data to the visualization environment, and on a controlled asynchronism between various components to improve interactivity. We managed to steer molecular systems of 1.7 M atoms at about 25 Hz using 384 CPU cores. This framework allowed us to study a concrete scientific problem by testing one hypothesis of the transport of an iron complex from the exterior of the bacteria to the periplasmic space through the FepA membrane protein.
Autres contacts
Institut de Biologie Physico-Chimique (IBPC)
13, rue Pierre et Marie Curie
75252 PARIS CEDEX 05