Associated Programs / -> Moloc Home

With the main executables Moloc and Molox comes a suite of associated programs which are located in the same directory (in Basel this directory is obtained by issuing the command: which mx). The following list gives a very short description of their purpose.
The usage of most programs is described, when they are started without any arguments.
NameFunction
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.
-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).