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 weights associated to the reconstructed conformational ensemble can be found in the notebook/output_check subfolder, both in binary and human-readable formats; the weights can also be easily recomputed and saved using dedicated instructions in the notebook. In the notebook/output_check/out_cluster_analysis subfolder, we supply representative structures, i.e. cluster centroids, for highest-weighted clusters from the reweighted ensemble in the form of individual PDBs, labelled with the corresponding cluster weight in the REMARK header line of each PDB; instructions to identify and save these structure files can be found inside the notebook as well. The notebook can also be easily consulted at https://github.com/CompMedChemLab/project_saxs-xlms-md_rad