Topology-based methods

Electron energies of coumarin and various isomers have been calculated by a onedimensional topology-based method, though it is recognized that such an approach to a multifunctional species can provide only a crude estimate of chemical reactivity (82JHC625). 

Four topologically based methods were used by Basak and GrunwaW in estimating the boiling point of a set of 139 hydrocarbons and a group of 15 nitrosamines using the nearest neighbor K = 1). 

Fugmann, R. Ploss, G. Winter, J.H. Supply of Information on Chemical Reactions. An Advanced, Topology-Based Method. J. Chem. Inf Comput. ScL, 1988,28, 47-53. 

A proper representation of the molecular structure is crucial for the prediction of spectra. Fragment-based methods, topological descriptors, physicochemical descriptors, and 3D descriptors have been used for this endeavor. 

A theoretical study on the reaction mechanism for the Bergman cyclization from the perspective of the Electron Localization Function and Catastrophe Theory has been reported.175 The authors argue that topological analysis of electron localization function can be used to complement the molecular orbital- or valence bond-based methods. 

Fariselli, P. Casadio, R. (1996). HTP a neural network-based method for predicting the topology of helical transmembrane domains in proteins. Comput Appl Biosci 12,41-8. 

In contrast to topological approaches, methods based on geometrical representations of molecular structures can be used instead. Among them, flexible superimposition of molecules onto one or multiple conformations of a reference bioactive ligand is a well-established methodology... 

Tree-building methods implemented in available software are discussed in detail in the literature (Saitou, 1996 Swofford et al., 1996 Li, 1997) and described on the Internet. This section briefly describes some of the most popular methods. Treebuilding methods can be sorted into distance-based vs. character-based methods. Much of the discussion in molecular phylogenetics dwells on the utility of distance-and character-based methods (e.g., Saitou, 1996 Li, 1997). Distance methods compute pairwise distances according to some measure and then discard the actual data, using only the fixed distances to derive trees. Character-based methods derive trees that optimize the distribution of the actual data patterns for each character. Pairwise distances are, therefore, not flxed, as they are determined by the tree topology. The... 

---