Preparation of Structures for Protein-Protein Docking

Although it is not necessary to prepare protein or nucleic acid structures for protein-protein docking, it may be advisable to do so. Structures from the PDB often do not have coordinates for side chains on the surface of the structure, or even for whole chains that are solvent-exposed, as these are usually more mobile and it can be difficult to determine their coordinates from the X-ray data. If these missing parts of the structure are not in the favored binding region, the docking should produce good results. If the poorly defined parts of the structure are in the binding domain, pre-docking preparation of the structure can appreciably improve results.

To prepare your structures for docking, you can use the Protein Preparation Workflow Panel. When you prepare your structure, you should select Fill in missing side chains to predict the side chains, and Fill in missing loops (using Prime) to predict the loops. The loop prediction used in the protein preparation is the faster look-up method, rather than the more extensive ab initio loop building. Both of these predictions can take several minutes.

In addition to fixing structural defects in the protein, you can also choose which het groups you want to keep in the structure. The het groups you keep are included in the final docked structures. You might, for example, want to keep ligands and cofactors, but remove compounds that were added for the crystallization.

If you are concerned about the accuracy of the surface side chains or loops, you can do a more extensive prediction in the Refinement panel (Protein Preparation and Refinement → Predict Side Chains, click the Tasks button and browse to Protein Preparation and Refinement → Refine Loops). If you have access to the X-ray data, you could consider performing some refinement of the structure with PrimeX, the X-ray refinement program. Choose Protein Preparation and Refinement → Protein X-Ray Refinement and use the toolbar to perform the refinement tasks. See the PrimeX User Manual — Contents for more information.

In the docking experiment, however, the accuracy of the methods may not be sufficient to distinguish between conformations, so an extensive prediction of the surface side chains or loops is probably not necessary. The presence of the side chain or loop in the right region is likely to be more important than its exact conformation. If you want to test the effects of loop or side chain conformations, you can generate multiple conformations and dock each of them.