Common Substructures Three Dimensional

It is interesting that in the 3-dimensional structures of them, obtained from X-ray diffraction data [24-26], they can be superimposed on one another at the point of the largest common substructure [31]. Figure 7 shows a three dimensional stereoscopic view of the common part of them, which were superimposed by the least squares method. 

Fig. 7. A stereoscopic view of the three-dimensional superimposition of the largest common substructure, (ii) in Fig. 6, among three narcotic analgesics...

In addition to investigations by mere structure overlapping methods and retrieval of three-dimensional substructures, there have been studies focused on developing an automated operation for recognizing common substructures, which takes into account the three-dimensional geometry of the molecules [49-54]. These approaches are greatly different from conventional one in that the designation of a query structure is not required. 

Brint, A.T. and Willett, P. (1987a). Algorithms for the Identification of Three-Dimensional Maximal Common Substructures. J.Chem.Inf.Comput.ScL, 27,152-158. 

G. Vriend and C. Sander. Detection of common three dimensional substructures in proteins. Proteins 77 52-58 (1991). 

Brint AT, Willett P. Algorithms for the identification of three-dimensional maximal common substructures. J Chem Inf Comput Sci 1987 27 152-158. 

Crandell CW, Smith DH. Computer-assisted examination of compounds for common three-dimensional substructures. J Chem Inf Comput Sci 1983 23 186-197. 

Chemical relationships (defined by say having one or more molecules or even molecular substructures in common) may be particularly difficult to detect, even if individual documents are visually inspected, since molecules may not be represented in a consistent, and hence comparable, manner. Thus some molecules may merely be named, either trivially or systematically others may be drawn as two-dimensional line diagrams with perhaps components such as the Markush R convention denoting a variable group which may be enumerated elsewhere. Three dimensional properties such as stereochemistry may be even less precisely or incompletely specified. 

These techniques often involve statistical treatment of data in a largely retrospective manner which is further limited by the arbitrary choice of common substructures, pharmacophores, binding points, and molecular overlays. In classical QSAR the limitations can be quite severe in that regressions are confined to a series of closely related structures often differing in relatively minor ways. More recent innovations Involve molecular shape analysis (13) and distance geometry methods (14). These techniques represent significant steps toward a true three-dimensional SAR with some predictive... 

Crandell, C.W. Smith, D.H. Computer-assisted Examination of Compounds for Common Three-dimensional Substructures . J. Chem. Inf. Comput. Sci. 1983,23, 186-197. 

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