Yu_Heidari_et_al_2026_molecular_dynamics_simulation_data_II
Year: 2025
Type: dataset
Abstract: ## Molecular Dynamics Simulation Dataset This dataset accompanies **Yu, Heidari et al. (2026)** and contains Martini 2.2 molecular dynamics models and simulation data for a single **NUP98 (aa 1–499)** chain, **NUP98 condensates**, and the **Nuclear Pore Complex (NPC)**. The dataset includes: 1. Representative structures and coordinates, together with measurements described in the associated publication;2. Selected simulation trajectories; and3. GROMACS input files required to set up and run the simulations. The dataset is organized into four main folders: ### 1. `Single_Chain` Contains the simulation setup and selected trajectories for a single NUP98 (aa 1–499) chain. ### 2. `Condensates` Contains the simulation setup and selected trajectories for NUP98 condensates. ### 3. `Martini_NPC` Contains the simulation setups and selected trajectories for the Martini 2.2 model of the NPC at different levels of O-glycosylation: * `f_0`: NPC without O-glycosylation (\(f_{\mathrm{gly}} = 0\))* `f_0.18`: NPC with an O-glycosylation fraction of \(f_{\mathrm{gly}} = 0.18\)* `f_0.3`: NPC with an O-glycosylation fraction of \(f_{\mathrm{gly}} = 0.30\)* `f_0.6`: NPC with an O-glycosylation fraction of \(f_{\mathrm{gly}} = 0.60\) ### 4. `Martini2_O-glycosylated_SER_THR_itps` Contains the Martini 2 `.itp` topology files for O-glycosylated serine (SER) and threonine (THR) residues. Detailed descriptions of the models, simulation protocols, and parameters are provided in the main text of the associated publication. ### Trajectory Files Each simulation folder contains a subfolder named: `0-Load_Last_Snapshots` This subfolder contains processed trajectories including only the NPC protein components; solvent and ion particles have been removed to reduce file size and facilitate visualization and analysis.
Institution: Max Planck Institute of Biophysics
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7208757893