Drug Design Toolbox software (DDT), a Matlab environment software developed in our group, allows calculation of the CoMSA molecular descriptors, PLS analysis, IVE-PLS variable elimination and molecular visualization.
DDT consists of two software layers. Firs layer performs all calculations and basic input – output operations including importing and exporting molecular data. All first layer functions can be accessed by Matlab command line and can be easily linked to other Matlab functions and scripts. Second layer is a graphical user interface. All calculations run by the second layer are accomplished by appropriate first layer functions. Thus, the second layer requires the first and the first can be used as stand alone command line only toolbox.
Our software is capable of importing and exporting molecular data form mol2 Sybyl files and ctx CACTVS files. However, during calculations DDT operates its own molecular format IQF (internal QSAR format). Similarly, data resulted form QSAR modeling are stored in DDT format, namely UQS (universal QSAR structure). Both formats, IQF and UQS, are XML based and can be saved as plain text files or in Matlab binary format. Moreover, in order to organize and simplify batch operations on huge molecular data DDT can create special directories QDB (QSAR data base) containing molecular series in IQF formats. Such directories can be easily accessed by DDT batch routines speeding up operations on huge molecular series.
The toolbox allows one a generation of the van der Waals molecular surfaces and a calculation of the electrostatic potential. However, partial charges have to be calculated using a third party software. There is ALOGP method implemented, thus a lipophilic potential can also be calculated using the slightly modified Audry et al. method.
Molecular descriptors can be calculated by grid (s-CoMSA) and SOM (SOM-CoMSA) formalisms, though, the freeware Kohonen SOM toolbox is required to use the latter method. DDT makes available several data preprocessing protocols. Quantitative modeling can be realized by PCR and PLS method. Both UVE-PLS and the several versions of IVE-PLS were implemented in DDT.
DDT is also a useful tool for molecular visualization, allowing to analyze the importance of the molecular surface sectors important for the activity. A variety of coloring maps are available as described in previous publications.
DDT web site is still under construction. We apologize for any inconvience.