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Tool: Dock Prep

Dock Prep performs several tasks to prepare structures for molecular docking or other calculations, such as:

Many of these steps can be performed separately, but Dock Prep unites them for convenience. The command implementation is dockprep. See also: AltLoc Explorer, Rotamers, Add Hydrogens, Add Charges, ViewDockX

If the atomic models to be prepared contain extra molecules such as ligands or additional subunits that are unwanted for further calculations, these extra molecules should be deleted before Dock Prep is used. Other than water and certain ions (optionally), Dock Prep does not delete them automatically in case they might be important. Conversely, the biological unit of the structure may contain more more subunits than are present in the input file. The relevant multimer should be obtained or generated beforehand, such as by fetching the PDB-biounit file or using the command sym. Finally, Dock Prep does not fill in any missing backbone segments. Short missing segments of a protein chain can be added with Model Loops, whereas longer missing segments can be predicted (in the context of a whole-chain prediction) with AlphaFold or ESMFold.

Dock Prep can be opened from the Structure Editing section of the Tools menu and manipulated like other panels (more...).

Structures to prep: The atomic model(s) to process should be chosen from the list. Processing options:

OK initiates processing and dismisses the dialog, whereas Cancel simply dismisses the dialog. Help opens this page in the Help Viewer.

UCSF Resource for Biocomputing, Visualization, and Informatics / November 2022