Substructure counts

There are several ways in which molecular descriptors can be classified. The majority of descriptors are atom-based rather than field-based. The bulk of this review is focused on a discussion of atom-based descriptors. As the name implies, atom-based descriptors are based on individual atoms, with the description extending outward to incorporate information about the atom s environment. The descriptors are typically generated by analysis of 2D or 3D connection tables, and can include ID, 2D, or 3D information about the molecule. Atom-based descriptors include individual atoms, feature counts, substructural fragments, topological indices, atomic properties, pharmacophores (see Chapters 17 and 18 of this book), and calculated physicochemical properties. 

Topological Representation and Topology), geometrical, electronic, and physicochemical. Topological de.scriptors are derived directly from the connection table repre.sentation of the structure and include atom and bond counts,. substructure counts, molecular connectivity indices (see Topological Indices), kappa indices, substructure environments, path descriptors, distance-sum connectivity, and molecular symmetry. Substructure-ba.sed descriptors are topological de.scriptors which allow the tailoring of the descriptor set to. specific user-defined substructures contained in the molecules of the data set. 

Substructural counts to flag compounds difficult to optimize (e.g. N02> 1,... 

Descriptors related to electronic effects counts of the positive (POS) and negative (NEG) ionic centers, based on fixed substructure searches (i.e., without predicting pK, ) ... 

Topoiogicai. Structure data that is based only on the connection table of the structure, without regard to 2D or 3D coordinates of the atoms. Examples include molecular weight and formula, counts of substructures, and indices like molecular connectivity. 

Both the functional group count and the fragment count can be derived from recognized substructures within the molecule, i.e. they are -> lD-descriptors in fact they are also considered specific -> substructure descriptors. 

Environment descriptors are closely related to - substructure descriptors, differing from the latter in using real values in place of binary variables or counts. The set of fragments is defined by the user depending on the data set and the specific problem. 

Kirchhoff matrix Laplacian matrix Kirchhoff number -> resistance matrix Klopman-Henderson cumulative substructure count... 

In general, substructure descriptors are the counts of predefined structural features in the molecules or binary variables specifying their presence/absence. 

Substructurai analysis is substructure searching where weights are calculated, relating the presence of a specific substructure moiety in a molecule to the probability that the molecule is active in some biological test system [Cramer III et al, 1974 Craig, 1990 Klopman, 1992]. Examples of substructurai analysis are the - Klopman-Hender-son cumulative substructure count and the -+ Hodes statistical-heuristic method. 

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