The Protein Preparation Process

The preparation of a protein involves a number of steps, which are outlined below. The procedure assumes that the initial protein structure is in a PDB-format file, includes a cocrystallized ligand, and does not include explicit hydrogens. The result is refined, and hydrogenated structures of the ligand and the ligand-receptor complex, suitable for use with other Schrödinger products, are written out. In many cases, not all of the steps outlined below need to be performed. These steps can be performed using the Protein Preparation Workflow Panel.

Import a ligand/protein cocrystallized structure, typically from the Protein Data Bank, into Maestro.

Locate any waters you want to keep, then delete all others.

These waters are identified by the oxygen atom, and usually do not have hydrogens attached. Generally, all waters (except those coordinated to metals) are deleted, but waters that bridge between the ligand and the protein are sometimes retained. If waters are kept, hydrogens are added to them in the preparation process.

Simplify multimeric complexes.

Determine whether the protein-ligand complex is a dimer or other multimer containing duplicate binding sites and duplicate chains that are redundant.
If the structure is a multimer with duplicate binding sites, remove redundant binding sites and the associated duplicate chains.

Adjust the protein, metal ions, and cofactors.

Fix any serious errors in the protein. Incomplete residues are the most common errors, but are relatively harmless if they are distant from the active site. Structures that are missing residues near the active site should be repaired.
Check the protein structure for metal ions and cofactors.
If there are bonds to metal ions, delete the bonds, then adjust the formal charges of the atoms that were attached to the metal as well as the metal itself.
Set charges and correct atom types for any metal atoms, as needed.
Set bond orders and formal charges for any cofactors, as needed.
Fix the orientation of any misoriented groups (such as amide groups of Asn and Gln).

Adjust the ligand bond orders and formal charges.

If you are working with a dimeric or large protein and two ligands exist in two active sites, the bond orders have to be corrected in both ligand structures.

Adjust the ionization and tautomerization state of protein and ligand, if necessary.

Refine the structure.

This step relieves any strain from the adjustments, and can also reorient groups.

Review the prepared structures.

Examine the refined ligand/protein/water structure for correct formal charges and protonation states and make final adjustments as needed.
Check the orientation of water molecules and other groups, such as hydroxyls, amides, and so on.