Protein Preparation

The typical structure file from the PDB is not suitable for immediate use in molecular modeling calculations. A typical PDB structure file consists only of heavy atoms and may include a cocrystallized ligand, water molecules, metal ions, and cofactors. Some structures are multimeric, and may need to be reduced to a single unit. Because of the limited resolution of X-ray experiments, it can be difficult to distinguish between NH and O, and the placement of these groups must be checked. PDB structures may be missing information on connectivity, which must be assigned, along with bond orders and formal charges.

Schrödinger has therefore assembled a set of tools to prepare proteins in a form that is suitable for modeling calculations. This manual describes these tools and their use in preparing proteins for various applications. The tools are combined in the Protein Preparation Workflow Panel. Procedures for manual adjustment and preparation of proteins are described in Manual Protein Preparation. You can also perform some tasks from the command line. The tools for doing this are described in the Protein Preparation Command Reference — Contents.

If you publish work that used the Protein Preparation tools, please use the citation listed on our citation page.