Docking with Moloc
General remarks
Moloc has a docking utility which can be accessed interactively
(lib/c) or in batch mode (program Mdck).
For efficient performance the user has to prepare a 'force' entry
beforehand which serves to preselect the conformations that fit
best into the cavity.
Force entries consist of force agons which are
displayed as sphere sections, represented as a sets of rings, each.
If switched 'active' they exert a force on atoms in dynamics runs
with the force field MAB (Their force cannot be derived from a
potential, whence they do not affect force-field minimization runs).
The forces are directed along the axes indicated by the centers of
the rings and point away from the sphere centers (imagine bumpers
of railway cars). However, these forces are only experienced by
atoms within the volume of the spheres of the agons.
Force entries are stored in .php file format, and their agons can
be modified in the pharmacophore menu 'php'
(position, direction and sphere radius).
In the context of docking, force entries are used to push ligand
molecules in proper position and modify their torsional angles
to optimally adapt to the shape of the cavity. They have no
pharmacophore properties by themselves and completely ignore
the ones of the ligands.
In addition, a final optimization step with the force field can be
applied, which optimizes and evaluates all detailed intermolecular
interaction. During this step the cavity atoms can optionally
and selectively also move under force field action (induced fit mode).
Preparing a Positions Entry
During a docking run molecules are initially positioned with their
centroids at the positions given by a positions entry. If no such entry
is given, the centroids of the molecules as given initially are taken as
starting positions.
- Position the structure of methotrexate into the display center.
- Enter menu 'php', choose menu item 'n'
and choose 'positions' as the entry type. A new empty
positions entry is opend and you will find yourself in the agon-insertion menu.
- You can enter an agon in the center of the display volume (option
'd') or on top of a picked atom (e.g. atom 'C6' of methotrexate B)
with option 'a'.
- An agon can be moved about with option 'm'. Pick it and
move it with the shift-key pressed.
- One can specify as many agons as thought necessary to explore a cavity
or target, e.g an additional one in the neiborhood of 'N1' of methotrexate.
The docking algorithm will choose all of them as starting positions.
- Save the positions entry as .php file '.../s/h'.
An example file 4dfr_B_ps.php can be found in the moloc/dat directory.
Preparing a Force Entry (optional)
- Proceed as in tutorial Fragment Positioning
where at first a reduced environment entry is generated.
This entry can also be utilized in the present context as the cavity
structure used in the final docking step.
- However, to produce an additional force entry select
'by distance and (max.) access' (instead of
'by distance, entire monomers', as before) and (possibly after some
impatient waiting for computations to be done) affirm the question for
the need of a 'force entry'.
- This force entry can be modified in the main menu
'php'. There should be only a minimal number of agons
needed to force the structures in optimal position and shape.
Thus, some of the automatically generated agons may possibly be removed
after some adjustment of position, direction, or volume of other agons.
- Since the cavity of 4dfr is rather wide (due to the missing structure
of NAD, it is advisable to add further force agons to prevent the inhibitors
from drifting away. Thus enter main menu 'php'.
- Select option 'a' (add and delete agons) and pick
an agon to specify the force entry to which further agons should be added.
- In the new menu, 'insert', select
'a' (add agon on top of a picked atom) and pick e.g. atom
'CB' of residue 'A19B' to obtain an additional agon at the corresponding
location.
- Exit to find yourself again in menu 'php' and move the
new agon about and orient it with the help of option 'k',
such that it helps to keep the molecules to be docked from drifting out of
the cavity. The agon radii may be modified with option 'r'.
- In addition the agon at 'CD1' of residue 'F31B' may also be moved in
a position suited to prevent ligand escape since its original function is
already covered by those of the agons at 'CD2' and 'CE1' of 'F31B'.
- Save the force entry as .php file '.../s/h'.
An example file 4dfr_B_frc.php can be found in the moloc/dat directory.
Interactive Docking
Now we have all ingredients for a docking run: force entry '4dfr_B_frc',
positions entry '4dfr_B_frc', and cavity (environment) entry '4dfr_B_env',
as well as a molecule, trimethoprim, to dock.
- Enter the library menu 'lib' and select
'c' (cavity docking). You will be presented with a list
of parameters which goverd the course of the docking process.
Accept the default values for the moment.
- Now a list of entries is presented from which the receptor cavity
is chosen. If no selection is made, the final minimization step will be
omitted. Choose 4dfr_B_env.
- Now the program asks for the force entry. If neither cavity nor force
entry is specified the program will stop. Choose 4dfr_B_frc.
- Now follows the specification of a positions entry to define initial
positions of the ligand centroid. Choose 4dfr_B_ps.
- Finally the structures to be docked have to be specifies.
Choose trimethoprim.
- Now the cavity entry is presented in the 'set' menu in order to define
the receptors atoms that should be kept fixed during the final minimization
step. Select the whole entry (option 'e' and picking).
Now the program docks tripethoprim into the cavity of DHFR. The steps of
this process can be described by interpreting the generated output:
trimethoprim
Parameters initialized for STANDARD force field!
1(2,2,1,1,1) 2 symmetries
672 cases: t 4(4), o 84, p 2
Max. extension 7.59
672 raw conformations
00000,46,2: -3.398e+001 -> -4.607e+001
01000,9,2: -2.790e+001 -> -3.874e+001
...
12 minimized
1 keep: 01000,35,2 -7.356e+001
The line after the molecular name characterizes the 5 torsional bonds and
the number of initial values for each (in brackets).
The next line gives the number of initial conformations (672), the product
of number of rotamers (4), orientations (84), and positions (2).
After processing by the force minimizer, which adjusts position, orientation
and torsional angles, the 672 raw conformations are juged by a coarse force
field evaluation (see below) and ranked correspondingly.
The top (12) cases are subjected to detailed minimization by the MAB force
field. The corresponding lines show the numbers of torsional bond settings,
of the orientation and of the position, then after the colon the coarse energy
and finally the result of minimization. A second ranking takes place and the
top structures (1) are kept in memory.
Batch Run Docking with Program Mdck
The batch programm Mdck expects the ligands in mol format (.sd). Furthermore,
the input .sd file must not contain explicit hydrogens nor multi-fragment
entries! Use Mol3d to prepare the input file.
- First store the initial structure of trimethoprim in the required
mol format: '.../s/n'.
- To keep the cavity atoms fixed, ensure (in the 'set' menu) that the
user set 'u0' is either empty, or contains all cavity atoms.
For 'induced-fit' type docking, specify the fixed atoms of the cavity
in set 'u0' and store the environment entry in .mab format. (At least one
atom must be kept fixed in this case!)
- Issue the following command to start the batch job:
Mdck -q 4dfr_B_env.mab -f 4dfr_B_frc -p 4dfr_B_ps trimethoprim.mol
Force and positions entries have unambiguous .php extensions. However,
for the cavity the extension must be specified, because all-atom type
(.mab) as well as pharmacophore type entries (.php) are allowed.
- The program produces a new file trimethoprim_dck.sd which contains
the same structure that was produced in the interactive run.
- The final energies are given in the .sd file under the data label
MDCK.
- Docking parameters may be changed by specification of the
corresponding program options. Help on the parameters can be obtained
By running: Mdck "?".
Coarse Force Field Energy Estimate
For the ranking of initial poses only non-bonded intermolecular interactions
are considered. All intramolecular terms of the ligand are omitted at that stage.
Two types of terms are evaluated:
- A van der Waals type energy between all pairs of atoms one from the
ligand the other from the receptor.
While the attractive part of the van der Waals potential is unchanged, the
repulsive part is drastically reduced to avoid rejection of small distance
cases. (At coincidence of atoms the energy reaches a maximum value of about
10 kcal/mol in a parabolic functional form. The minimum of the parabola is located
at the van der Waals minimum.) This is done with the (not unjustified) expectation
that the final minimization will take care of close atomic approaches without too
much loss in binding energy.
- H-bond energies between ligand and receptor.
The H-bond interaction is modified to the extent that minimal
energies are unchanged, but ranges are increased (by a factor 2.5 in distance
and 1.75 in angles) in order to capture potential H-bonds that are still somewhat
off in geometry. Again the expectation is that the final minimization will adjust
atomic positions to optimal H-bond geometries.