Structural flexibility of the human vault particle revealed by high-resolution cryo-EM and molecular dynamics simulations

This repository contains the raw data and simulation files supporting the molecular dynamics (MD) simulations presented in the paper: "Structural flexibility of the human vault particle revealed by high-resolution cryo-EM and molecular dynamics simulations." The dataset is organized into two main components: Figures 5 & 6 Reproduction Package (zip file):Includes all structures and VMD (Visual Molecular Dynamics) script files necessary to reproduce Figures 5 and 6 from the manuscript. Simulation Input and Output Data (zip file): Initial structures: All-atom and coarse-grained (CG) starting models for both the primed and committed states of the full vault and half-vault particles in PDB format. Simulation setup files: .mdp configuration files used for production runs in both all-atom and coarse-grained simulations. Trajectories: Production trajectories for each replicate, sampled every 1 ns for all-atom simulations and every 1.5 ns for coarse-grained simulations provided in XTC format. Contact information:Name: Karen Palacio-RodriguezInstitution: Department of Theoretical Biophysics, Max Planck Institute of BiophysicsAddress: Max-von-Laue-Str. 3, 60438 Frankfurt am Main, GermanyEmail: [email protected]