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

Related Organizations

Université Paris Cité
France
French National Centre for Scientific Research
France
University of Lyon System
France

Keywords

Molecular Dynamics Simulations, protein-protein interactions

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