Computer software QSAR

The first stage includes the selection of a dataset for QSAR studies and the calculation of molecular descriptors. The second stage deals with the selection of a statistical data analysis and correlation technique, either linear or nonlinear such as PLS or ANN. Many different algorithms and computer software are available for this purpose in all approaches, descriptors serve as independent variables and biological activities serve as dependent variables. 

Complete enumeration of each type of subgraph becomes computationally intense as structure complexity increases. All the necessary computations are carried out by computer software along with calculations for many other quantities of interest in QSAR. ... 

CODESSA reads molecular structure files or output files created by other software packages as the starting point for QSAR analysis. It can import computational results from AMPAC, MOPAC, and Gaussian as well as structures in a number of common formats. 

Chemoinformatics (or cheminformatics) deals with the storage, retrieval, and analysis of chemical and biological data. Specifically, it involves the development and application of software systems for the management of combinatorial chemical projects, rational design of chemical libraries, and analysis of the obtained chemical and biological data. The major research topics of chemoinformatics involve QSAR and diversity analysis. The researchers should address several important issues. First, chemical structures should be characterized by calculable molecular descriptors that provide quantitative representation of chemical structures. Second, special measures should be developed on the basis of these descriptors in order to quantify structural similarities between pairs of molecules. Finally, adequate computational methods should be established for the efficient sampling of the huge combinatorial structural space of chemical libraries. 

QSAR models created with SVMs are best utilized in Binary QSAR applications to determine if compounds are bioactive for the system of interest as is the case with high throughput screening. The Binary QSAR method of Binary-QuaSAR (7,41) of the Chemical Computing Group, Inc., is the best example of a Binary QSAR application, and is provided with the software suite MOE (28). 

Comparative molecular field analysis (CoMFA) is a modern, powerful extension of the classical QSAR methods that were developed in the 1960s.14 While Hansch analysis is simple to understand and fairly easy for any medicinal chemist to perform, CoMFA requires specialized software and an understanding of statistics. Since CoMFA is outside the experience of most synthetic chemists, pharmaceutical companies have dedicated computational chemistry groups to handle advanced QSAR tasks. 

Ivanciuc, O. and Devillers, J. (2000). Algorithms and Software for the Computation of Topological Indices and Structure-property Models. In Topological Indices and Related Descriptors in QSAR and QSPR (Devillers, J. and Balaban, A.T, eds.), Gordon Breach, Amsterdam (The Netherlands), pp. 779-804. 

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