Name | Function |
Moloc |
To get help on startup options, issue the command: Moloc -h |
Gr2d |
draws 2-dimensional plots of several curves.
Input file format |
- | .sd-File Handling |
Mngsd |
Exploration, modification of .sd-files. |
Mfltr |
Structures can be filtered out of a .sd-file with respect
to varous properties. |
Mdfy |
Simple modifications of structures can be performed. |
- | Minimization, Structure Generation |
Mabch |
runs a MAB force-field minimization (or dynamics calculation)
and is usually started from within Moloc. |
Mcbch |
Runs a C-alpha force field minimization or dynamics calculation. |
Mol3d |
Produces a .sd file containing 3-dimensional coordinates from
a 2-dimensional .sd file. It can also be used for post-minimization
of structures, e.g. after docking into a receptor. |
Msmab |
Produces a file (.mab, .sd, or .tdt) of 3-dimensional structures
with partial atomic charges from a list of smiles codes. |
Mcnf |
Generates conformations via a random variation of atom coordinates
followed by energy minimization.
|
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- | Docking |
Mdck |
Docking program of Moloc. This is a batch version of Moloc's option
'lib/c'. To obtain extended help, it is recommended to work through an
interactive example
(see corresponding tutorial). |
- | Similarity, Topological Pharmacophore |
M3dsml |
Performs similarity calculations on conformations of structures from
files. Overlap and H-bonding properties are considered utilizing a
3d-superposition algorithm. |
Mtprgn |
Produces a topological pharmacophore representation (.tpr file)
for a set of structures (e.g. a database).
(about topological pharmacophores) |
Mtprsml |
Performs similarity calculations on topological pharmacophore
files (.tpr). These are useful in clustering problems or for
database searches (examples). |
Mtprcnt |
Counts the distribution of topological pharmacophores stored on
.tpr files in terms of numbers of hydrophobic and hydrophillic
agons. I allows to write a file with the name of structures that
will be omitted when restricting the overall size of
pharmacophores in similarity calculations (Mtprsml). |
Mabxtr |
Extracts coordinates of a list of structures from a set of
pool coordinate files. Mostly used after tpr-database searches, (ROSIS),
where structures are kept for all entries in the database.
The list file may be a .tdt file which results from a search (r400.tdt).
|
Mphmch |
Matches a set of structures onto a target by topological
pharmacophore similarity cryteria. |
- | Clustering |
Mtree |
reads a triangular similarity matrix (Moloc format),
performs a hierarchical clustering and writes the result in Newick
format or as a table. |
Mclsn |
reads a similarity file (Moloc format),
performs partitional clustering(s), based on shared near neighbors,
and writes the result as a table. |
- | Linear Models |
Msrfvl |
Calculates various descriptors for a set of structures given as
a .mol (.sd) file. Legend to Msrfvl
gives an interpretation of the resulting table for an example selection
of descriptors (generated with option -hgd1000). |
Mtprmp |
Calculates model predictions for a set of structures given in
.mol(.sd) format. The program requires additional files relating
to the topological pharmacophore model, which must be generated beforehand
(see corresponding tutorial). |
Mmdls |
Allows to calculate properties of structures from minimal linear models
installed with the Moloc package. The structures must be provided through
an .sd-file. |
Mndrws |
Calculates an average binding energy for a set of structures given in
.mol(.sd) format.
It assumes that all pharmacophoric groups take part in binding.
Parametrization is after
P.R.Andrews, D.J.Craik, and J.L.Martin, J.Med.Chem. 27, 1648 (1984).
Correct protonation of the structures is very important, because
charged groups give large contributions. |
- | Special |
Mamber |
Takes a .mol2 (.mol, .sd) file as input and produces three files
(.dat, .lib, and .so) suited for AMBER input, for each structure found
on the input file. Charges are taken from the MAB algorithm, with a free
choice of the parameters 'h' and 'd'. |
Mfebd |
Calculates binding entropies. This program is used for MMPBSA-type
calculation in connection with the corresponding AMBER utility. |
Mbcd |
Transforms a Moloc pharmacophore file (.php) to a .hed file which is the
command file to start BIOCAD's HYPEDIT program. In a proper environment
HYPOEDIT is started to produce a hypothesis with which a CATALYST database
search is issued. |
Mdltcat |
Filters DAYLIGHT thor output from the catalog972 database for
availability of compounds from a list of suppliers. |
Mltwk |
Performs lattice-walk calculations. This program was used to explore
the effect of pegylation of proteins on their stability
(Bioconjugate Chem., 16 (3), 518 -527, 2005). |