Indicator descriptors

TOPIX Software Development Lohninger www.lohninger.com/topix.html Simple constitutional descriptors, topological indices, descriptors of substructures (augmented atoms)... 

The first group of descriptors consists of the directional WHIM size (or d-WSIZ indices) descriptors defined as the - eigenvalues Xi, X2 and X3 of the weighted covariance matrix of the molecule atomic coordinates they account for the molecular size along each principal direction. 

The second group consists of the directional WHIM shape (or d-WSHA indices) descriptors i i, i 2 and calculated as eigenvalue ratios and related to molecular shape ... 

The third group of descriptors consists of the directional WHIM symmetry (or d-WSYM indices) descriptors Yj, Y2 73> calculated as -+ mean information content on the symmetry along each component with respect to the centre of the scores ... 

The total number of indicator descriptors (i.e., the Free-Wilson matrix columns) is... 

QuaSAR descriptors [QuaSAR - Chemical Computing Group, Inc., 2007] include several types of traditional molecular descriptors Kier-Hall —> connectivity indices, —> structural keys. Estate indices, descriptors of physico-chemical properties (such as log P, molecular weight and molar refractivity), 3D molecular features (such as potential energy descriptors, surface area, volume and —> shape descriptors, conformation dependent partial charge descriptors), and some pharmacophore-based descriptors. 

The average aroma intensity differences from the blanched reference are illustrated in Figures 2a,b,c. When the average aroma intensity was not different from the reference, the value on the y-axis would be 50, as shown by the horizontal line. The length of the vertical bar represents the degree of lesser or greater intensity difference from the reference. The cross-hatched bars indicate descriptors that were statistically different from the blanched reference. 

CoMSIA similarity indices descriptors were derived according to Klebe et al. [18] with the same lattice box used for the CoMFA. CoMSIA similarity indices (Ap) for a molecule j with atoms i at a grid point q are determined as follows ... 

Figure 2-74. Basic stages for describing a stereoisomer by a permutation descriptor. At the stereocenter, the molecule is separated into the skeleton and its ligands. Both are then numbered independently, with the indices of the skeleton in italics, the indices of the ligands in bold.

As another example, we shall consider the influence of the number of descriptors on the quality of learning. Lucic et. al. [3] performed a study on QSPR models employing connectivity indices as descriptors. The dataset contained 18 isomers of octane. The physical property for modehng was boiling points. The authors were among those who introduced the technique of orthogonahzation of descriptors. 

There was a time when one could use only a few molecular descriptors, which were simple topological indices. The 1990s brought myriads of new descriptors [11]. Now it is difficult even to have an idea of how many molecular desaiptors are at one s disposal. Therefore, the crucial problem is the choice of the optimal subset among those available. 

Usually, the denominator, if present in a similarity measure, is just a normalizet it is the numerator that is indicative of whether similarity or dissimilarity is being estimated, or both. The characteristics chosen for the description of the objects being compared are interchangeably called descriptors, properties, features, attributes, qualities, observations, measurements, calculations, etc. In the formiilations above, the terms matches and mismatches" refer to qualitative characteristics, e.g., binary ones (those which take one of two values 1 (present) or 0 (absent)), while the terms overlap and difference" refer to quantitative characteristics, e.g., those whose values can be arranged in order of magnitude along a one-dimensional axis. 

Z eb index, Wiener index. Balaban J index, connectivity indices chi (x), kappa (k) shape indices, molecular walk counts, BCUT descriptors, 2D autocorrelation vector... 

Some further topological descriptors are the Kier-Hall connectivity indices [13] and the electrotopological state index (or -state index) [14]. A comprehensive overview of topological molecular desaiptors is given by Todeschini and Consonni [15]. 

As explained in Chapter 8, descriptors are used to represent a chemical structure and, thus, to provide a coding which allows electronic processing of chemical data. The example given here shows how a GA is used to Rnd an optimal set of descriptors for the task of classification using a Kohoncii neural network. The chromosomes of the GA are to be used as a means for selecting the descriptors they indicate which descriptors are used and which are rejected ... 

The model building step deals with the development of mathematical models to relate the optimized set of descriptors with the target property. Two statistical measures indicate the quality of a model, the regression coefficient, r, or its square, r, and the standard deviation, a (see Chapter 9). 

Table 12.2 A list of some of the more common descriptors. Details of some of these descriptors can be found elsewhere as indicated. This table is restricted to those descriptors which can be computed it therefore excludes certain classes (such as the Hammett substituent constants) which are derived from experimental studies (sec Section 12.12).

Many of the descriptors which can be calculated from the 2D structure rely upon the molecular graph representation because of the need for rapid calculations. Kier and Hall have developed a large number of topological indices, each of which characterises the molecular structure as a single number [Hall and Kier 1991]. Every non-hydrogen atom ir the molecule is characterised by two delta values, the simple delta Si and the valence delta SJ ... 

Topological Indices and Related Descriptors in QSAR and QSPR J. Devillers, A. T. 

Other techniques that work well on small computers are based on the molecules topology or indices from graph theory. These fields of mathematics classify and quantify systems of interconnected points, which correspond well to atoms and bonds between them. Indices can be defined to quantify whether the system is linear or has many cyclic groups or cross links. Properties can be empirically fitted to these indices. Topological and group theory indices are also combined with group additivity techniques or used as QSPR descriptors. 

The S in S adenosylmethio nine indicates that the adenosyl group is bonded to sulfur It does not stand for the Cahn-Ingold-Prelog stereochemical descriptor... 

Boranes are usually named by indicating the number of B atoms with a latin prefix and the number of H atoms by an arabic number in parentheses, e.g. B5H9, pentaborane(9) B5H11, pentaboranefl 1). Names for anions end in ate rather than ane and specify both the number of H and B atoms and the charge, e.g. BsHs" octahydropentaboratefl—). Further information can be provided by the optional inclusion of the italicized descriptors closo-, nido-, arachno-, hypho- and conjuncto-, e.g. ... 

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