The docking functionality uses a hybrid scheme of the FlexX docking
and a force field (amber+gaff) optimisation.
The same scheme as employed by FlexX was used to generate the placement
of the base fragment.
So first distance tables are generated to store
all the distances between the interaction points in the protein.
The protein has to be supplied in a pdb format with hydrogens present.
Molden can be used to generate such a pdb file.
For now, the orientation
of for example OH groups (Serine,Threonine,tyrosine) have to be predefined.
The user can define a sphere around a to be picked point, which encloses
all the interaction points which are relevant for the docking.
These interaction point can be either H(ydrogen Bond)_Acc(eptor),
H(ydrogen Bond)_Don(onor) or aromatic/ch(2,3).
The user selected
amino acid residues are then assigned interaction points.
For each combination of interaction groups, distances are collected and
stored in a distance table.
Next a ligand must be supplied in ambfor .xyz format (molden own force
field format), also charges must have been assigned for proper force
field scoring.
Next interaction points are assigned to the ligand. From these, interaction
triples are generated.
This list of triples is searched against the distance
tables to find matching protein interaction triples,
these are called base fragments.
For the ligand, two to three interaction points are generate for each
OH group, One for each rotamer.
Initially the ligand is divided up into fragments. Fragments are typically
connected by single SP3-SP3 or SP2-SP3 bonds.
These fragments are stored
internally by molden.
This fragmentation is used to generate different
conformations of the ligand by rotating around the dihedral angles of the
single bonds separating the fragments.
The bonds that are not strict
single bonds (SP2-SP3) are kept in order to carry out a complete scan of the energy
with respect to these dihedrals.
For regular SP3-SP3 bonds the standard
angles of the staggered conformations of ethane are employed.
When the debug button is pressed in the "Docking Start" window a file
called "conformers.mol2" is written.
The orientation of the base fragment is very important for the following
steps in the docking procedure.
That is why the base fragment placement
is optimised to obtain a near perfect placement.
If we have a base fragment
consisting of all Hydrogen bond acceptors and donors, the van der waals
part of the force field scoring is reduced,
so that the orientation is
dominated by electrostatic part of the force field scoring.
If we were dealing with a base fragment with one pair of Hydrogen bond
acceptors or donors and one hydrophobic interaction point,
we rotate
around the axis formed by this pair to find the energetically optimal angle for
the remaining hydrophobic interaction point with respect to the pair.
Because the hydrophobic interaction between hydrophobic interaction points
are much smaller than between a acceptor and donor pair
(round about
seven times weaker) and are much less well defined in space, the optimal
placement is rarely the one found in the original base placement,
but
will be impacted more by the rest of the ligands placement.
The main scheme assumes a base fragment that has
interaction points belonging to the same fragment. This is by far the
fastest docking scheme.
Here we map the base fragment onto the earlier
created conformers (Debug: mconformers.mol2),
followed by an optimisation
of the conformers along the dihedrals of the non-pure single bonds
that molden stored earlier.
However when a ligand triplet with two or more Hydrogen bond acceptor/donor
interaction points can not be formed from the same fragment, a different
docking scheme is employed.
Now we use the whole of the conformations of the ligand to sample ligand
points,
but to make the algoritm more efficient we only keep the unique
ones
(unique by location of the interaction points
origin) and store the conformations it belongs to with these interaction
points.
After optimisation of the base fragments, the ligand poses are
generated from the combined confomer information of the three interaction
points.
If all three interaction points contain the same conformer,
this conformer is mapped onto the base fragment,
followed by an optimisation
of the conformers along the dihedrals of the non-pure single bonds
that molden stored earlier.
The force field scoring is stored into the multi-mol result dock.mol2
file.
The source distribution of molden5.8 has a 'dock' subdirectory of the test
directory, with three different docking:
CAVEATS/Missing functionality: