'Ab ovo' building of structures
General Remarks
This tool allows to build structures by connecting fragments
in a tree topology. Fragments are collected in various libraries
for which various parameters are set, such as minimum an maximum
number of occurence of fragments and relative frequency of
selection from each library. Consequently, the resulting
structures depend strongly on the type of structures found in
the libraries and on library parameters.
The libraries must exist beforehand and can be produced,
most conveniently by decomposing known structures and filtering
the resulting fragments for various properties
(template generation).
Interactive structure building can be performed in menu
'Dyn/o'. In addition, the program Movo allows
to run the algorithm in batch mode.
Building a Cage
- into a cavity
- Start Moloc with the environment entry for DHFR
(see moloc/dat directory): Moloc -c 4dfr_B_env.mab
- Enter the pharmacophore menu 'Php' and
select the void-into-cavity item, 'V' and
pick the entry. This puts you into the set menu in order to
choose atoms from which the void generating process starts out.
- Specify atoms CD1 of the amino acid F31B, OD2 of D27B, and
CG2 of T46B. They are positionned such, that starting from them
the cavity can be filled reasonably well. Exit from the set menu.
- From the parameters which can be set now, the range is
most important. It determined how far away the cage agons spill
from the start atom, and should correspond with the selection
of start atoms. A value of about 6 is appropriate here.
- around ligand(s)
- Start Moloc and read in the inhibitor entry '4dfr_B_MTX' from
the file 4dfr.pdb.
- H-counts may be set correctly (dTp/h) if proper agon types
in the generated cage entry are needed.
- Enter the pharmacophore menu 'Php', choose
'v'.
- Choose the inhibitor in the selector window. If required,
several entries can be selected (eg. superimposed ligands).
- Not all parameters appearing in the parameter table have
an effect in this mode of the void algorithm (eg. range).
- At the end of the void insertion process, the radii of all
agons can be simultaneously scaled.
- A new pharmacophore, cg_4dfr_B_env (cg_4dfr_B_MTX), is
generated with several agons that map out the protein site
(ligand volume).
- The cage may be modified by deleting, moving, or adding
agons. For open cavities, as in our case, it is usually
necessary to remove quite a few agons, which have spillt
to far into open space.
- This entry will provide the potential to keep bounded the
positons of the molecules to be built.
- You may visualize the corresponding potential in the map
utility 'Map': generate map with
'q', contour with 'k'.
Specification of Libraries
- Moloc-generated libraries
(.mab files) must be listed in a .ils file and can be read in
'Dyn/o/l/g' (see help text there for format rules
for the .ils file). 'moloc/dat/flx.ils' is an examle.
- In addition to libraries, the extensions encountered in their
fragments must be specified. This is done by reading a file,
by default called 'LABEL'. The program asks for such a file when
reading libraries. A default file 'LABEL_moloc' is found in Moloc's
data directory 'moloc/dat'.
- Libraries can be listed, 'l', browsed through,
'b', or searched for extension types,
'e'.
- Fragments are energy-minimized during reading by default, in order
to eliminate biases. Option 'f' allows to check
the fragment bias-energies.
- The 'moloc/dat' directory is searched for library files which have
not been found in the working directory. Two small libraries,
lnk.mab (linkers) and r1_pl.mab (planar single-ring templates), are
provided there as examples.
- Libraries in Roche's convention (compatible with the program
SKELGEN) can be read in 'Dyn/o/G'. The environment
variable, SKELGEN, which is expected to point to the corresponding
directory is also understood by Moloc.
- A library can be specified as 'fixed' or 'constrained' in the .ils
file (see help of 'Dyn/o/g'). A template from such
a seed library is either held fixed or
constrained to its initial position during structure building.
In this mode of operation, each structure contains exactly one such
fragment. The file 'moloc/dat/dfr_sd.mab' is an example of a library
with two fragments suited as fixed or constrained seeds.
Building Structures Interactively
- Before starting a building run, choose option 'q'.
There, the libraries are selected which are to be used to build up
the structures. Furthermore, the cage (compulsory), which specifies
the building volume, as well as (optionalyy) cavity- and target
entries are specified. If a cage has been specified the programm
proceeds automatically to option 'p'.
- Parameter specification 'p' presents a large set
of parameters in several tables. A detailed description can be found
in the help texts of these tables.
- At the end the program asks whether a options file is wanted (eg.
my.ovopar). This file lists the parameters with non-default values
in a format that can be read by the batch program 'Movo'.
- Building starts with option 's', where first the
number of structures to be built must be specified.
- For testing purposes, if only a single structures is asked for,
the program stops after every change in fragments for examination.
Furthermore, a new option, 'h', becomes avaliable
in the end, by which the built structure can be represented in
fragment specific coloring.
- Building starts from a fixed or constrained template if such a
library is specified. Alternatively, when a target is specified, the
first template (seed) is positionned onto it. Otherwise, the seed
is put on top of a cage agon, preferentially onto a center one.
Building Structures in Batch Mode
The Program 'Movo' is used to run a building process in batch mode.
In the present examples the starting commands for bulding 100
structures would read:
- Cavity case:
Movo -N100 -l mylibs.ils -k cg_4dfr_B_env.php -q 4dfr_B_env.mab
+my.ovopar tst100
- Template case:
Movo -N100 -l mylibs.ils -k cg_4dfr_B_MTX.php -s 4dfr_B_MTX.mab
+my.ovopar tst100
The specification of libraries, cage, and entries etc. can,
of course, also be edited into the options file.