Yasaman KARAMI – Nancy Computational Structural Biology (NCSB) meeting

Learning the sequence embedding space for scalable host-pathogen protein interaction prediction

Yasaman KARAMI 2026/01/19 2026/01/19Abstracts

Luiz Felipe Piochi1, Di Tang2, Johan Malmström2, Yasaman Karami1, Hamed Khakzad1,* 1 Université de Lorraine, CNRS, Inria, LORIA, F-54000 Nancy, France2 Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine,Lund University, Lund, Sweden AbstractProtein-protein interaction (PPI) prediction remains sparse for bacteria and host-pathogen systems, limiting mechanistic insight…

NCSB 2025

Yasaman KARAMI 2026/01/19 2026/01/19Previous editions

We are happy to announce that the second NCSB will be held on June 19th, 2025 at Nancy , with the support of the Centre Inria de l’Universite de Lorraine, LORIA and GDR BIMMM. We have the pleasure of hosting internationally distinguished experts in computational and structural biology. Here is…

Enhancing Protein Binding Site Prediction with Dynamic Features and Surface-Core Discrimination

Yasaman KARAMI 2025/04/07 2025/04/07Abstracts

Omid Mokhtari Inria, Loria, CNRS, Universite de Lorraine, Nancy Proteins are dynamic entities, and their conformational flexibility, particularly in intrinsically disordered regions (IDRs), plays a crucial role in their function. While significant progress has been made in predicting protein-protein interfaces, existing methods often overlook conformational heterogeneity. We employ state-of-the-art geometric…

Accurate binder design using BindCraf

Yasaman KARAMI 2025/03/22 2025/03/22Abstracts

Martin Pacesa LPDI, EPFL, Switzerland Protein–protein interactions (PPIs) are at the core of all key biological processes. However, the complexity of the structural features that determine PPIs makes their design challenging. We present BindCraft, an open-source and automated pipeline for de novo protein binder design with experimental success rates of…

Exploring epigenetic mechanisms with all-atom MD simulations

Yasaman KARAMI 2025/03/22 2025/03/22Abstracts

BIGNON Emmanuelle;A QIU Yuya;A SMIRNOVA Ekaterina;B SCHULTZ Patrick;B PAPAI Gabor;B BEN SHEM AdamB A) Université de Lorraine and CNRS, UMR 7019 LPCT, Nancy, France; B) Department of Integrated Structural Biology, IGBMC, CNRS and INSERM, UMR 7104-UMR-S 1258, Illkirch, France emmanuelle.bignon@univ-lorraine.fr Gene activity is tightly controlled by reversible chemical modifications called…

Modelling host-pathogen interactions using multiscale MD simulations: the Mycobacterium tuberculosis case

Yasaman KARAMI 2025/03/22 2025/03/22Abstracts

Matthieu Chavent Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse 31400, France Mycobacterium tuberculosis, the pathogen responsible for the infectious disease tuberculosis, is known for its thick and waxy envelope constituted of numerous complex lipids (1). These lipids act both…

Structural insights into chromatin modifiers and remodeles

Yasaman KARAMI 2025/03/22 2025/03/22Abstracts

Patrick Schultz IGBMC, UMR 7104 CNRS, U1258 INSERM, Université de Strasbourg Changqing Li, Ekaterina Smirnova, Charlotte Schnitzler, Corinne Crucifix, Arnaud Poterszman, Patrick Schultz, Gabor Papaiand Adam Ben-Shem, in collaboration with Jean Paul Concordet (Museum National d’Histoire Naturelle, U 1154 Inserm, UMR 7196 CNRS) Chromatin structure is a key regulator of…

Martini 3: A journey through development and future prospects

Yasaman KARAMI 2025/03/22 2025/03/22Abstracts

Paulo C. T. Souza Laboratoire de Biologie et Modélisation de la Cellule, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, Centre Blaise Pascal de Simulation et de Modélisation Numérique, 46 Allée d’Italie, 69364, Lyon, France. The Martini model is among the most popular…

Program – NCSB 2024

Yasaman KARAMI 2025/03/22 2025/03/22Program

Here is the program of NCSB 2024 (click on each title to read the abstract): 9:30 – 9:45: Welcome and introduction9:45 – 10:30: Massimiliano Bonomi (Institut Pasteur, CNRS, Paris) – Protein structural ensembles from 3D and 2D cryo-EM data10:30 – 11:00: Coffee break11:00 – 11:30: Chris Chipot (Université de Lorraine,…

NCSB 2024

Yasaman KARAMI 2025/03/22 2025/03/22Previous editions

We are happy to announce that the second NCSB will be held on July 9th at Nancy , with the help of the LORIA and Inria. We have the pleasure of hosting internationally distinguished experts. Here is the program. Please remember to register! Registration is free but mandatory! The seminar will…