Computing a desired suite of indices in this Windows-based programming environment basically involves three steps entailing three files. You specify the appropriate Meqi II Programming Template options, save the template as a CSV command file, and run the Meqi executable. The image in the upper-left corner of this page is an example of a programming template for computing the frameworks, ring systems, linkers and side-chains discussed in Bemis and Murcko (J.Med.Chem, 39(1996)2887). The designations of the two output files, CyclicSystems.sdf and RngsSchsBrdgs.sdf, are only needed if you want the mol files of the computed cyclic systems, ring systems, side chains and bridges. Your program, the CSV command file, is accessible to your proprietary softwarve via a simple call to the Meqi II executable.
The following downloads provide different glimpses on how Meqi II can be used to explore chemotypes and their use in drug discovery.
Meqi II: A Template-Based Programming Environment for Computing Chemotypic Indices - a poster presented at the 2006 Midwest Biopharmaceutical Statistics Workshop that briefly introduces the notion of a chemotypic index, presents the basic programming template and closes with a few simple, but illustrative applications of some typical indices. (Last updated 8/17/2006)
The Meqi Data Sets - A zip file of small, but diverse and illustrative data sets taken from public sources that are used throughout the examples discussed in these downloads. (Last updated 8/17/2006)
Our Introduction to the MeqiSuite Indices provides a first look at chemotypic analysis that defines, illustrates and suggestively applyies a number of different chemotypic indices in typical drug-discovery contexts. These indices can be computed using the preprogrammed Meqi template MeqiSuite. This template computes 62 command indices and 4 hierarchical orderings for general use. (Last updated 8/23/2007)
A Brief Introduction to RingSystemSuite provides a more in depth look at issues related to hierarchically ordering compounds in a manner for viewing and analyzing HTS data when ring systems are thought to play an important role in activity. These indices can be computed using the preprogrammed Meqi template RingSystemSuite. Six different hierarchical orderings are discussed. (Last updated 3/24/2009)
The Meqi II Programming Template and Its Underlying Chemotypic Concepts reviews the use of chemotypes in pharmaceutical discovery, presents the underlying concepts, and describes the Meqi template-based programming language for specifying and computing them. (Last updated 8/20/2007)
Specifying and Using Hierarchically-Organized Structural Categories a poster presented at the 2003 GRC on Computer-Aided Drug Discovery giving a brief, though somewhat dated introduction to chemotypic indices but also containing a very preliminary, yet interesting comparison of different chemotypic classes with respect to their likelihood of containing a member closely associated with the critical substructure of a marketed drug selected at random from 13 therapeutic categories included in the 12th edition of the Merck Index. (Last updated 5/2/2008)
The Meqi programming templates contain a simple Excel macro for saving the programming template as a CSV file. If your firewall prevents you from downloading a file containing an Excel macro, please contact us to work out another arrangement.