Structure Representation Topological

Computation Structural Applications Spectroscopic Databases Standard Exchange Formats for Spectral Data Structure Databases Structure Determination by Computer-based Spectrum Interpretation Structure Representation Topological Methods in Chemical Structure and Bonding, ... 

The problem of perception complete structures is related to the problem of their representation, for which the basic requirements are to represent as much as possible the functionality of the structure, to be unique, and to allow the restoration of the structure. Various approaches have been devised to this end. They comprise the use of molecular formulas, molecular weights, trade and/or trivial names, various line notations, registry numbers, constitutional diagrams 2D representations), atom coordinates (2D or 3D representations), topological indices, hash codes, and others (see Chapter 2). 

The importance of methods to predict log P from chemical structure was described in Chapter 14, which is focused on fragment- and atom-based approaches. In this chapter property-based approaches are reviewed, which comprise two main categories (i) methods that use three-dimensional (3D) structure representation and (ii) methods that are based on topological descriptors. 

Votano, J.R., Parham, M., Hall, L.H., Kier, L.B., Hall, L.M. Prediction of aqueous solubility based on large datasets using several QSPR models utilizing topological structure representation. Chem. Biodivers. 2004, 1, 1829-41. 

Generally speaking, 3D QSAR approaches provide useful tools for drug design and virtual screening. However, in many cases they require one to go back to topology-based (2D or 2.5D) structure representation rather than analyze the 3D molecular models directly. 

This group of methods includes methods that use the 3D structure representation of molecules, such as CLIP [88], QikProp [89], COSMOlogP [47,48], as well as methods based on topological indexes calculated for the whole... 

Topological graphs are concerned only with which nodes (atoms) are joined by which edges (bonds), thus have difficulty in representing stereochemistry directly. A number of approaches have been used to incorporate information about stereochemical configuration into chemical structure representations. ... 

With this definition, we can consider the structure representations of molecules in Section 7.2 as topological descriptors. At present, more than 5000 molecular descriptors can be computed [5]. They can be categorized by their data types (Table 7.11) or by their dimensionality (Table 7.12). 

L. M. Hall, L. H. Hall and L. B. Kier, Modeling drug albumin binding affinity with E-state topological structure representation, /. Chem. Inf. Comput. Set, 2003, 43, 2120-2128. 

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