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