tpr-Databases in Basel / -> Topological Pharmacophors

Search-Scripts

There exist the following scripts located in the Moloc bin-directory at the Basel site. (obtain the directory path by issuing the command 'which mx'). They access the following databases:

Each of these databases exist in two different levels of coarseness.
The resolution parameter of the search scrips selects in the following way: For consistency it is advisable to use the corresponding parameter values for generation of the .tpr file of the query structure (Moloc option php/v,w, or Mtprgn).
Of course, the program Mtprgn can also be used to build up user specific databases.

Modifying Scripts

It is possible to modify any of the scripts to adjust to special needs such as modified maximum number of pharmacophors, or modifies parameters for the similarity calculation. To obtain the meaning of the parameters start Mtprsml without arguments.

Running Scripts

The scripts are designed to run in parallel on all partitions of a database (8 for the case of Rosis). Thus, do NOT run these scripts on a single processor machine! It will be hopelessly overloaded. In such circumstances parallel running must be avoided by removing the &-signs from the script.
The scripts return a full similarity file ranked with respect to a substructure type search (second number, column 3), a top-400 .tdt file to interface DAYLIGHT software, and a top-400 .mab file of 3-d structures.

Remarks

CPU-times for similarity calculations with topological pharmacophors grow very quickly with increasing number of agons. The default value of 8 yields reasonable times (few minutes). If the search pharmacophor is small, the limit may be increased (leading to larger pharmacophors of the base to be included). This makes usually only sense, if the substructure type surch is of interest.
In general, with rather large lead structures, a more coarse grained description must be chosen to achieve reasonable search times. On the other hand, the fine grained description is suited to look for more detailed analogs of smaller structures or fragments.