Protein-Protein Docking

The question of whether one protein (or nucleic acid structure) binds to another, and where, can be addressed by protein-protein docking. Protein-protein docking in BioLuminate is performed using the Piper program [5], under license from Boston University. The job can be set up in the Protein-Protein Docking Panel (Biologics → Protein-Protein Docking). In this panel you can set up jobs to dock two arbitrary protein or nucleic acid (DNA/RNA) structures, dock an antigen to an antibody, or dock one protein to itself to form a dimer or a trimer.

One structure is treated as the “receptor” and the other as the “ligand”. In the general case, it does not matter which structure is treated as the receptor and which is treated as the ligand. For antibody-antigen docking, the receptor is the antibody and the ligand is the antigen. The algorithm samples all possible orientations of the two structures, subject to whatever constraints are applied. It uses a grid to locate the best poses of the two structures, with a maximum resolution in the poses of about 5°. The docking is performed as a rigid-body optimization: there is no subsequent minimization of the interfacial region. If you want to optimize the interface after docking, you can select the residues at the interface using the Quick Select tools in the Workspace, and use the selection for a minimization or refinement.

Some information on preparing structures and using restraints is given in the topics listed below.