The Protein Preparation Workflow

Many of the protein preparation tasks can be performed automatically with the Protein Preparation Workflow. The Protein Preparation Workflow Panel allows you to take a protein from its raw state, (which may be missing hydrogen atoms and have incorrect bond order assignments, charge states, or orientations of various groups) to a state in which it is properly prepared for use by Schrödinger products such as Glide, Prime, QSite, and MacroModel.

The panel has two modes: Automatic and Interactive. The default is Automatic, where a job is submitted to a queue using the standard Job Toolbar, and can prepare multiple structures with the same settings. Interactive mode, where you can run individual parts of the workflow, is entered by clicking the Interactive button.

The Protein Preparation Workflow Panel has three tabs, which contain tools for the stages of protein preparation. In the Preparation Workflow tab, you can import a protein and perform the basic tasks for fixing the structures; optimize orientations of hydrogen-bonded groups, delete waters, and minimize the structure. The Substructures tab allows you to delete unwanted chains and waters, and fix or delete het groups. The Diagnostics tab provides information on problems with the structure. For an unprocessed protein, such as one imported from the PDB, you should run through the entire workflow. If your protein has no missing atoms and has the bond orders assigned already, you may be able to skip steps in the workflow.

Because automatic procedures cannot cover all possible cases, it is very important to check the correctness of the structure before using it for other applications. The Workflow helps you to do this by allowing you to step through various parts of the system and check their correctness. For each task completed, the Workflow adds a Boolean property to the structure, so you can track what has been done. Procedures for manual checking and correction of structures are given in Manual Protein Preparation.

To open the Protein Preparation Workflow Panel, choose Protein Preparation and Refinement → Protein Preparation Workflow, or click the Protein Preparation button on the Favorites toolbar (if present).

To open the Protein Preparation Workflow Panel when you have imported a PDB structure, you can click the Prepare link in the banner that is displayed after import.

For information on using the Protein Preparation Workflow, see the Protein Preparation Workflow Panel topic.