"The molecular descriptor is the final result of a logic and mathematical procedure which transforms chemical information encoded within a symbolic representation of a molecule into a useful number or the result of some standardized experiment." (Handbook of Molecular Descriptors, R.Todeschini and V.Consonni, Wiley-VCH, 2000).
Molecular descriptors play a fundamental role in chemistry, pharmaceutical sciences, environmental protection policy, health research and quality control, they being obtained when molecules are transformed into a molecular representation allowing some mathematical treatment. Many molecular descriptors have been proposed derived from different theories and approaches with the aim of predicting biological and physico-chemical properties of molecules [R.Todeschini and V.Consonni, Handbook of Molecular Descriptors, Wiley-VCH, Weinheim (GER), 2000].
The information content of a molecular descriptor depends on the kind of molecular representation that is used and on the defined algorithm for its calculation. There are simple molecular descriptors derived by counting some atom-types or structural fragments in the molecule, other derived from algorithms applied to a topological representation (molecular graph) and usually called topological or 2D-descriptors, and there are molecular descriptors derived from a geometrical representation that are called geometrical or 3D-descriptors.
All the molecular descriptors must contain, to varying extents, chemical information, must satisfy some basic invariance properties and general requirements, and must be derived from well-established procedures which enable molecular descriptors to be calculated for any set of molecules. It is obvious – almost trivial - that a single descriptor or a small number of descriptors cannot wholly represent the molecular complexity or model all the physico-chemical responses and biological interactions. As a consequence, although we must get used to living with approximate models (nothing is perfect!), we have to keep in mind that "approximate" is not a synonym of "useless".
The field of molecular descriptors is strongly interdisciplinary and involves a variety of different theories. For the definition of molecular descriptors, a knowledge of algebra, graph theory, information theory, computational chemistry, theories of organic reactivity and physical chemistry is usually required, although at different levels. For the use of the molecular descriptors, a knowledge of statistics, chemometrics, and the principles of the QSAR/QSPR approaches is necessary in addition to the specific knowledge of the problem.
The 29 logical molecular descriptors blocks (and their sub-blocks) calculated by Dragon are:
|3.1.||Vertex degree-based indices|
|4.2.||Self-returning walk counts|
|5.1.||Kier-Hall molecular connectivity indices|
|5.2.||Solvation connectivity indices|
|5.3.||Randic-like connectivity indices|
|6.2.||Indices of neighborhood symmetry|
|7.||2D matrix-based descriptors|
|7.2.||Topological distance matrix|
|7.5.||Reciprocal squared distance matrix|
|8.2.||Centred Broto-Moreau autocorrelations|
|8.5.||Topological charge autocorrelations|
|10.4.||Van der Waals volume|
|12.||Edge adjacency indices|
|14.||3D matrix-based descriptors|
|14.1.||Geometrical distance matrix|
|14.2.||Reciprocal squared geometrical distance matrix|
|16.3.||Weighted by van der Waals volume|
|16.4.||Weighted by Sanderson electronegativity|
|16.5.||Weighted by polarizability|
|16.6.||Weighted by ionization potential|
|17.3.||Weighted by van der Waals volume|
|17.4.||Weighted by Sanderson electronegativity|
|17.5.||Weighted by polarizability|
|17.6.||Weighted by ionization potential|
|20.||Randic molecular profiles|
|21.||Functional group counts|
|23.||Atom-type E-state indices|
|25.1.||Weighted topological atom pairs|
|25.3.||Frequency Atom Pairs|
|26.1.||Weighted geometrical atom pairs|