Enhanced-sampling MD simulations of the RAD51-BRC4 complex

Molecular dynamics simulations of the RAD51-BRC4 complex, using enhanced sampling methods (steered MD and metadynamics). The simulations integrate experimental information, namely SAXS (in the steered MD) and XL-MS (in the metad). All input files necessary to perform the simulations are provided, including the initial model of the full RAD51-BRC4 complex generated via AlfaFold2 after proper equilibration, used to start the steered MD, as well as the output files (including MD trajectories). In the notebook folder, we also provide a Jupyter Notebook to analyze results and perform ensemble reweighting through the maximum entropy principle; the folder also gathers all files necessary to run the notebook and a lighter version of the trajectories. The content of the notebook folder can also be found at https://github.com/CompMedChemLab/project_saxs-xlms-md_rad