Tool: Dock Prep

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

• deleting water molecules
• repairing truncated sidechains
• adding hydrogens
• assigning partial charges

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:

• Delete solvent – delete any solvent molecules (usually waters). This is generally done to prepare a receptor structure for docking. If any solvent molecules are thought to be important for ligand binding, however, one should manually delete the other solvent residues beforehand and deactivate this option in Dock Prep.
  
  
• Delete non-complexed ions – delete any monatomic ions that are not participating in covalent or coordination bonds (by default, the latter are shown as dashed lines). This bonded-or-not distinction is based solely on input bond specifications such as CONECT and LINK records in PDB files; it is not inferred from the chemistry of the system.
  
  
• “Standardize” certain residue types – whether to convert the following nonstandard residues to the corresponding standard types:
  • selenomethionine (MSE) → methionine (MET) – change the selenium atom to a sulfur atom named SD and adjust the CG-SD and SD-CE bond lengths to 1.81 and 1.78 Å, respectively
  • bromo-UMP (5BU) → UMP (U) – change 5-bromouridine-5'-monophosphate to RNA residue uridine-5'-monophosphate by deleting the bromine atom
  • methylselenyl-dUMP (UMS) → UMP (U) – replace the methylselenyl moiety with an oxygen atom named O2' and adjust the bond length to 1.430 Å
  • methylselenyl-dCMP (CSL) → CMP (C) – replace the methylselenyl moiety with an oxygen atom named O2' and adjust the bond length to 1.430 Å
  
  
• Incomplete side chains (see Rotamers for more details on the rotamer libraries):
  • Replace using Dunbrack rotamer library (default) – Dunbrack 2010 smooth backbone-dependent rotamer library (5% stepdown; for chain-terminal residues, the Dunbrack 2002 backbone-independent version is used instead)
  • Replace using Dynameomics rotamer library – Dynameomics rotamer library
  • Replace using Richardson (common-atom) rotamer library – common-atom values (author-recommended) from the Richardson backbone-independent rotamer library
  • Replace using Richardson (mode) rotamer library – mode values from the Richardson backbone-independent rotamer library
  • Mutate residues to ALA (if CB present) or GLY – convert amino acid residues with truncated sidechains to alanine (leave only sidechain -CH₃, if present, otherwise mutate to glycine, which does not have a sidechain)
  • Mutate residues to GLY – convert amino acid residues with truncated sidechains to glycine (remove sidechain entirely)
  
  
• Add hydrogens – whether to call Add Hydrogens
  
  
• Add charges – whether to call Add Charges
  
  
• Write Mol2 file – open a dialog for saving a Mol2 file

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