Code and scripts for the alpha-synuclein idp dimer manuscript

manuscipt_scripts/:

1. Structure alphabet calucations: analyse_hotspots.ipynb, markov_hotspots.py, sa.in, transition_probability.in, trim_clusters.sh, voronota.sh,
2. Docking:active_passive.sh, execute_haddock.sh, generate_run.sh, par_run.sh, rescore.sh,weights_it0.ipynb.
3. Simulations:rmsd_matrix_plot.ipynb, simulation.sh, *.mdp, compute_rg.sh, compute_hbonds.sh, compute_contacts.sh.
4. Markov State Modelling: gnn4.ipynb, make_graphs_500ns.py,mermaid_training.md, transformerconv.py.

Other relevant scripts:

α-Synuclein dimerisation scripts

1. RosettaDock + Restrained Docking + MD + analysis scripts are here.
2. Voronoi tesselation, Structural alphabet, beta propensity scripts are pending.