A dynamical view of protein-protein complexes: studies by molecular dynamics simulations

All-atom MD simulations generated for the manuscript "A dynamical view of protein-protein complexes: studies by molecular dynamics simulations". Eight binary protein-protein complexes from the Docking benchmark and the Affinity benchmark are studied in this work: 2OOB (an ubiquitin/ubiquitin ligase complex), 1AY7 (a ribonuclease Sa/barstar complex), 1BRS (a barnase/barstar complex), 3SGB (a proteinase B/inhibitor), 1EMV (a colicin/immunity protein complex), 1PVH  (complex between Interleukine 6 receptor and leukemia inhibitory factor), 1GCQ (Vav/GRB2 SH3 domains complex) and 1AK4 (cyclophilin/HIV capsid complex)

Each folder for a binary complex is organised as followed:

- in A and B there are the dry MD simulations for the unbound proteins

- in complex there are two folders (without_water and water) where the dry simulation and the simulation with water molecules are provided